File: hhsuite-userguide.bib

package info (click to toggle)
hhsuite 3.0~beta2%2Bdfsg-3
  • links: PTS, VCS
  • area: main
  • in suites: stretch
  • size: 19,352 kB
  • ctags: 5,085
  • sloc: cpp: 24,813; ansic: 12,868; perl: 12,233; python: 938; makefile: 163; sh: 14
file content (2478 lines) | stat: -rw-r--r-- 72,900 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
1650
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
1728
1729
1730
1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
1756
1757
1758
1759
1760
1761
1762
1763
1764
1765
1766
1767
1768
1769
1770
1771
1772
1773
1774
1775
1776
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
1787
1788
1789
1790
1791
1792
1793
1794
1795
1796
1797
1798
1799
1800
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
1821
1822
1823
1824
1825
1826
1827
1828
1829
1830
1831
1832
1833
1834
1835
1836
1837
1838
1839
1840
1841
1842
1843
1844
1845
1846
1847
1848
1849
1850
1851
1852
1853
1854
1855
1856
1857
1858
1859
1860
1861
1862
1863
1864
1865
1866
1867
1868
1869
1870
1871
1872
1873
1874
1875
1876
1877
1878
1879
1880
1881
1882
1883
1884
1885
1886
1887
1888
1889
1890
1891
1892
1893
1894
1895
1896
1897
1898
1899
1900
1901
1902
1903
1904
1905
1906
1907
1908
1909
1910
1911
1912
1913
1914
1915
1916
1917
1918
1919
1920
1921
1922
1923
1924
1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
1936
1937
1938
1939
1940
1941
1942
1943
1944
1945
1946
1947
1948
1949
1950
1951
1952
1953
1954
1955
1956
1957
1958
1959
1960
1961
1962
1963
1964
1965
1966
1967
1968
1969
1970
1971
1972
1973
1974
1975
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2022
2023
2024
2025
2026
2027
2028
2029
2030
2031
2032
2033
2034
2035
2036
2037
2038
2039
2040
2041
2042
2043
2044
2045
2046
2047
2048
2049
2050
2051
2052
2053
2054
2055
2056
2057
2058
2059
2060
2061
2062
2063
2064
2065
2066
2067
2068
2069
2070
2071
2072
2073
2074
2075
2076
2077
2078
2079
2080
2081
2082
2083
2084
2085
2086
2087
2088
2089
2090
2091
2092
2093
2094
2095
2096
2097
2098
2099
2100
2101
2102
2103
2104
2105
2106
2107
2108
2109
2110
2111
2112
2113
2114
2115
2116
2117
2118
2119
2120
2121
2122
2123
2124
2125
2126
2127
2128
2129
2130
2131
2132
2133
2134
2135
2136
2137
2138
2139
2140
2141
2142
2143
2144
2145
2146
2147
2148
2149
2150
2151
2152
2153
2154
2155
2156
2157
2158
2159
2160
2161
2162
2163
2164
2165
2166
2167
2168
2169
2170
2171
2172
2173
2174
2175
2176
2177
2178
2179
2180
2181
2182
2183
2184
2185
2186
2187
2188
2189
2190
2191
2192
2193
2194
2195
2196
2197
2198
2199
2200
2201
2202
2203
2204
2205
2206
2207
2208
2209
2210
2211
2212
2213
2214
2215
2216
2217
2218
2219
2220
2221
2222
2223
2224
2225
2226
2227
2228
2229
2230
2231
2232
2233
2234
2235
2236
2237
2238
2239
2240
2241
2242
2243
2244
2245
2246
2247
2248
2249
2250
2251
2252
2253
2254
2255
2256
2257
2258
2259
2260
2261
2262
2263
2264
2265
2266
2267
2268
2269
2270
2271
2272
2273
2274
2275
2276
2277
2278
2279
2280
2281
2282
2283
2284
2285
2286
2287
2288
2289
2290
2291
2292
2293
2294
2295
2296
2297
2298
2299
2300
2301
2302
2303
2304
2305
2306
2307
2308
2309
2310
2311
2312
2313
2314
2315
2316
2317
2318
2319
2320
2321
2322
2323
2324
2325
2326
2327
2328
2329
2330
2331
2332
2333
2334
2335
2336
2337
2338
2339
2340
2341
2342
2343
2344
2345
2346
2347
2348
2349
2350
2351
2352
2353
2354
2355
2356
2357
2358
2359
2360
2361
2362
2363
2364
2365
2366
2367
2368
2369
2370
2371
2372
2373
2374
2375
2376
2377
2378
2379
2380
2381
2382
2383
2384
2385
2386
2387
2388
2389
2390
2391
2392
2393
2394
2395
2396
2397
2398
2399
2400
2401
2402
2403
2404
2405
2406
2407
2408
2409
2410
2411
2412
2413
2414
2415
2416
2417
2418
2419
2420
2421
2422
2423
2424
2425
2426
2427
2428
2429
2430
2431
2432
2433
2434
2435
2436
2437
2438
2439
2440
2441
2442
2443
2444
2445
2446
2447
2448
2449
2450
2451
2452
2453
2454
2455
2456
2457
2458
2459
2460
2461
2462
2463
2464
2465
2466
2467
2468
2469
2470
2471
2472
2473
2474
2475
2476
2477
2478
@Article{Remmert:2010,
author = {Remmert, M. and Biegert, A. and Linke, D. and Lupas, A. and S\"oding, J.},
title = {Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin},
year = "2010",
journal = "Mol. Biol. Evol.",
volume = "27",
pages = "1348-1358",
}

@article{Higgins:2011,
  title={{Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega}},
  author={Higgins, D. and Sievers, F. and Wilm, A. and Dineen, D. and Gibson, T. and Karplus, K. and Li, W. and Lopez, R. and  McWilliam, H. and Remmert, M. and Söding, J. and Thompson J.},
  journal={Mol Syst Biol.},
  year={201]1},
  volume={7},
  pages={539}
}
 
@article{uniprot:2010,
  title={{The Universal Protein Resource (UniProt) in 2010}},
  author={{UniProt Consortium}},
  journal={Nucleic Acids Res.},
  year={2010},
  volume={38(Database issue)},
  pages={D142-148}
}

@article{Marks:2011,
  title={Protein {3D} Structure Computed from Evolutionary Sequence Variation},
  author={Marks, D. and Colwell, L.J. and Sheridan, R. and Hopf, R.A. and Pagnani, A. and Zecchina, R. and Sander C.},
  journal={PLoS ONE},
  year={2011},
  volume={24},
  pages={807-814}
}

@Article{Remmert:2011,
  Author = {Remmert, M. and Biegert, A. and Hauser, A. and {\bf S\"oding, J.}},
  Title = {HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment},  
  Year = "2011",
  Journal = "Nat. Methods",
  Volume = "9",
  Pages = "173-175"
}  

@article{Mariani:2011,
  title={Assessment of template based protein structure predictions in {CASP9}},
  author={Mariani, V. and Kiefer, F. and Schmidt, T. and Haas, J. and Schwede, T.},
  journal={Proteins},
  volume={79(Suppl 10)},
  number={1},
  pages={37–58},
  year={2011},
}

@article{Aydin:2011,
  title={Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure},
  author={Aydin, Z. and Singh, A. and Bilmes, J. and Noble, W.},
  journal={BMC Bioinformatics},
  volume={12},
  number={1},
  pages={154},
  year={2011},
}

@article{Hegyi:2001,
  title={Annotation transfer for genomics: measuring functional divergence in multi-domain proteins},
  author={Hegyi, H. and Gerstein, M.},
  journal={Genome Res.},
  volume={11},
  number={10},
  pages={1632-1640},
  year={2001},
}


@article{Soding:2011,
  title={Protein sequence comparison and fold recognition: progress and good-practice benchmarking},
  author={S{\"o}ding, J. and Remmert, M.},
  journal={Curr. Opin. Struct. Biol.},
  volume={21},
  pages={401-411},
  year={2011},
}


@article{Zemla:2001,
  title={{Processing and evaluation of predictions in CASP4}},
  author={Zemla, A. and Venclovas, {\v{C}}. and Moult, J. and Fidelis, K.},
  journal={Proteins},
  volume={45},
  number={S5},
  pages={13-21},
  year={2001}
}

@Article{Melvin:2011,
author = "Melvin, I. and Weston, J. and Noble, W. S. and Leslie, C.",
title = {Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding},
journal = "PLoS Comput. Biol.",
year = "2011",
volume = "7",
number = "",
pages = "e1001047",
}

@Article{Kummerfeld:2009,
author = "Kummerfeld, S. K. and Teichmann, S. A.",
title = {Protein domain organisation: adding order},
journal = "BMC Bioinformatics",
year = "2009",
volume = "10",
number = "",
pages = "39",
month = "",
pmid = "19178743",
}

@Article{Margelevicius:2010,
author = "Margelevicius, M. and Venclovas, C.",
title = {Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison},
journal = "BMC Bioinformatics",
year = "2010",
volume = "11",
number = "",
pages = "89",
month = "",
pmid = "20158924",
}

@Article{Sadreyev:2009,
author = "Sadreyev, R. I. and Tang, M. and Kim, B. H. and Grishin, N. V.",
title = {COMPASS server for homology detection: improved statistical accuracy, speed and functionality},
journal = "Nucleic Acids Res.",
year = "2009",
volume = "37",
number = "Web Server issue",
pages = "90-94",
month = "Jul",
pmid = "19435884",
}


@article{Moult:2009,
  title={{Critical assessment of methods of protein structure prediction -- Round VIII}},
  author={Moult, J. and Fidelis, K. and Kryshtafovych, A. and Rost, B. and Tramontano, A.},
  journal={Proteins},
  volume={77},
  number={S9},
  pages={1-4},
  year={2009},
}

@Article{Alva:2010,
author = "Alva, V. and Remmert, M. and Biegert, A. and Lupas, A. N. and S{\"o}ding, J.",
title = {A galaxy of folds},
journal = "Protein Sci",
year = "2010",
volume = "19",
pages = "124-130",
month = "Jan",
pmid = "19937658",
}

@Article{Qi:2007,
author = "Qi, Y. and Sadreyev, R. I. and Wang, Y. and Kim, B. H. and Grishin, N. V.",
title = {A comprehensive system for evaluation of remote sequence similarity detection},
journal = "BMC Bioinformatics",
year = "2007",
volume = "8",
pages = "314-314",
month = "",
pmid = "17725841",
}

@article{Frank:2010,
  title={{COPS Benchmark: interactive analysis of database search methods}},
  author={Frank, K. and Gruber, M. and Sippl, M. J.},
  journal={Bioinformatics},
  volume={26},
  pages={574-575},
  issn={1367-4803},
  year={2010},
  publisher={Oxford Univ Press}
}

@Article{Cuff:2011,
author = "Cuff, A. L. and Sillitoe, I. and Lewis, T. and Clegg,  A. B. and Rentzsch, R. and Furnham, N. and Pellegrini-Calace, M. and Jones, D. and Thornton, J. and Orengo, C. A.",
title = {{Extending CATH: increasing coverage of the protein structure universe and linking structure with function}},
journal = "Nucleic Acids Res.",
year = "2011",
volume = "39",
pages = "D420-426",
month = "Jan",
pmid = "20843957",
}

@Article{Andreeva:2008,
author = "Andreeva, A. and Howorth, D. and Chandonia, J. M. and Brenner, S. E. and Hubbard, T. J. and Chothia, C. and Murzin, A. G.",
title = {Data growth and its impact on the SCOP database: new developments},
journal = "Nucleic Acids Res.",
year = "2008",
volume = "36",
pages = "D419-425",
month = "Jan",
pmid = "18000004",
}

@Article{Chubb:2010,
author = "Chubb, D. and Jefferys, B. R. and Sternberg, M. J. and Kelley, L. A.",
title = {Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe},
journal = "Bioinformatics",
year = "2010",
volume = "26",
pages = "2664-2671",
month = "Nov",
pmid = "20843957",
}

@Article{Heger:2007,
author = "Heger, A. and Mallick, S. and Wilton, C. and Holm, L.",
title = {The global trace graph, a novel paradigm for searching protein sequence databases},
journal = "Bioinformatics",
year = "2007",
volume = "23",
pages = "2361-2367",
month = "Sep",
pmid = "17823134",
}

@Article{Uversky:2010,
author = "Uversky, V. N. and Dunker, A. K.",
title = {Understanding protein non-folding},
journal = "Biochim Biophys Acta",
year = "2010",
volume = "1804",
pages = "1231-1264",
month = "Jun",
pmid = "20117254",
}

@Article{Jung:2009,
author = "Jung, I. and Kim, D.",
title = {{SIMPRO: simple protein homology detection method by using indirect signals}},
journal = "Bioinformatics",
year = "2009",
volume = "25",
pages = "729-735",
month = "Mar",
pmid = "19164303",
}

@Article{Bateman:2007,
author = "Bateman, A. and Finn, R. D.",
title = {{SCOOP: a simple method for identification of novel protein superfamily relationships}},
journal = "Bioinformatics",
year = "2007",
volume = "23",
pages = "809-814",
month = "Apr",
pmid = "17277330",
}

@Article{Rangwala:2005,
author = "Rangwala, H. and Karypis, G.",
title = {Profile-based direct kernels for remote homology detection and fold recognition},
journal = "Bioinformatics",
year = "2005",
volume = "21",
pages = "4239-4247",
month = "Dec",
pmid = "16188929",
}

@Article{Melvin:2009,
author = "Melvin, I. and Weston, J. and Leslie, C. and Noble, W. S.",
title = {{RANKPROP: a web server for protein remote homology detection}},
journal = "Bioinformatics",
year = "2009",
volume = "25",
pages = "121-122",
month = "Jan",
pmid = "18990723",
}

@Article{Weston:2004,
author = "Weston, J. and Elisseeff, A. and Zhou, D. and Leslie, C. S. and Noble, W S",
title = {Protein ranking: from local to global structure in the protein similarity network},
journal = "Proc Natl Acad Sci U S A",
year = "2004",
volume = "101",
pages = "6559-6563",
month = "Apr",
pmid = "15087500",
}

@Article{Eddy:2008,
author = "Eddy, S. R.",
title = {A probabilistic model of local sequence alignment that simplifies statistical significance estimation},
journal = "PLoS Comput. Biol.",
year = "2008",
volume = "4",
pages = "e1000069",
month = "May",
}

@Article{Johnson:2010,
author = "Johnson, L. S. and Eddy, S. R and Portugaly, E.",
title = {{Hidden Markov model speed heuristic and iterative HMM search procedure}},
journal = "BMC Bioinformatics",
year = "2010",
volume = "11",
pages = "431-431",
month = "",
pmid = "20718988",
}

@Article{Farrar:2007,
author = "Farrar, M.",
title = {{Striped Smith-Waterman speeds database searches six times over other SIMD implementations}},
journal = "Bioinformatics",
year = "2007",
volume = "23",
pages = "156-161",
month = "Jan",
pmid = "17110365",
}

@Article{Gonzalez:2010,
author = "Gonzalez, M. W. and Pearson, W. R.",
title = {Homologous over-extension: a challenge for iterative similarity searches},
journal = "Nucleic Acids Res.",
year = "2010",
volume = "38",
pages = "2177-2189",
month = "Apr",
pmid = "20064877",
}

@Article{Lee:2008,
author = "Lee, M. M. and Chan, M. K. and Bundschuh, R.",
title = {{Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches}},
journal = "Bioinformatics",
year = "2008",
volume = "24",
pages = "1339-1343",
month = "Jun",
pmid = "18403442",
}

@article{Frith:2008,
  title={{The whole alignment and nothing but the alignment: the problem of spurious alignment flanks}},
  author={Frith, M. C. and Park, Y. and Sheetlin, S. L. and Spouge, J. L.},
  journal={Nucleic Acids Res.},
  volume={36},
  pages={5863-5871},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{Peng:2010,
  title={{Low-homology protein threading}},
  author={Peng, J. and Xu, J.},
  journal={Bioinformatics},
  volume={26},
  pages={i294-300},
  issn={1367-4803},
  year={2010},
  publisher={Oxford Univ Press}
}

@Article{Xia:2009,
author = "Xia, X. and Zhang, S. and Su, Y. and Sun, Z.",
title = {{MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields}},
journal = "Bioinformatics",
year = "2009",
volume = "25",
pages = "1433-1434",
month = "Jun",
pmid = "19359356",
}

@article{Kim:2010,
  title={{Learning models for aligning protein sequences with predicted secondary structure}},
  author={Kim, E. and Wheeler, T. and Kececioglu, J.},
  journal ={Journal of Computational Biology},
  volume = "17", 
  pages={561-580},
  year={2010},
}

@article{Do:2006,
  title={{CONTRAlign: discriminative training for protein sequence alignment}},
  author={Do, C. and Gross, S. and Batzoglou, S.},
  booktitle={Research in Computational Molecular Biology},
  journal = "Lecture Notes in Computer Science",
  volumne = "3909",
  pages={160-174},
  year={2006},
  organization={Springer}
}

@Article{Altschul:2010,
author = "Altschul, S. F. and Wootton, J. C. and Zaslavsky, E. and Yu, Y. K.",
title = {The construction and use of log-odds substitution scores for multiple sequence alignment},
journal = "PLoS Comput. Biol.",
year = "2010",
volume = "6",
pages = "e1000852",
month = "",
pmid = "20657661",
}

@Article{Altschul:2009,
author = "Altschul, S. F. and Gertz, E. M. and Agarwala, R. and Sch{\"a}ffer, A. A. and Yu, Y. K.",
title = {{PSI-BLAST pseudocounts and the minimum description length principle}},
journal = "Nucleic Acids Res.",
year = "2009",
volume = "37",
pages = "815-824",
month = "Feb",
pmid = "19088134",
}

@Article{Laganeckas:2010,
author = "Laganeckas, M. and Margelevicius, M. and Venclovas, C.",
title = {{Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments}},
journal = "Nucleic Acids Res.",
year = "2010",
month = "Oct",
pmid = "20961958",
doi = "10.1093/nar/gkq958"
}

@Article{Wang:2009,
author = "Wang, Y. and Sadreyev, R. I. and Grishin, N. V.",
title = {{PROCAIN: protein profile comparison with assisting information}},
journal = "Nucleic Acids Res.",
year = "2009",
volume = "37",
pages = "3522-3530",
month = "Jun",
pmid = "19357092",
}

@Article{Sadreyev:2008,
author = "Sadreyev, R. I. and Grishin, N. V.",
title = {{Accurate statistical model of comparison between multiple sequence alignments}},
journal = "Nucleic Acids Res.",
year = "2008",
volume = "36",
pages = "2240-2248",
}

@Article{Dlakic:2009,
author = "Dlakic, M.",
title = {{HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch}},
journal = "Bioinformatics",
year = "2009",
volume = "25",
pages = "3071-3076",
month = "Dec",
pmid = "19773335",
}

@Article{Boekhorst:2007,
author = "Boekhorst, J. and Snel, B.",
title = {Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties},
journal = "BMC Bioinformatics",
year = "2007",
volume = "8",
pages = "356-356",
month = "",
pmid = "17888146",
}

@Article{Fokkens:2010,
author = "Fokkens, L. and Botelho, S. M. and Boekhorst, J. and Snel, B.",
title = {{Enrichment of homologs in insignificant BLAST hits by co-complex network alignment}},
journal = "BMC Bioinformatics",
year = "2010",
volume = "11",
pages = "86-86",
month = "",
pmid = "20152020",
}

@Article{Fornes:2009,
author = "Fornes, O. and Aragues, R. and Espadaler, J. and Marti-Renom, M. A. and Sali, A. and Oliva, B.",
title = {{ModLink+: improving fold recognition by using protein-protein interactions}},
journal = "Bioinformatics",
year = "2009",
volume = "25",
pages = "1506-1512",
month = "Jun",
pmid = "19357100",
}

@Article{Abeln:2007,
author = "Abeln, S. and Teubner, C. and Deane, C. M.",
title = {Using phylogeny to improve genome-wide distant homology recognition},
journal = "PLoS Comput. Biol.",
year = "2007",
volume = "3",
pages = "e3",
month = "Jan",
pmid = "17238281",
}

@Article{Huang:2006,
author = "Huang, Y. M. and Bystroff, C.",
title = {Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions},
journal = "Bioinformatics",
year = "2006",
volume = "22",
pages = "413-422",
month = "Feb",
pmid = "16352653",
}

@Article{Lobley:2009,
author = "Lobley, A. and Sadowski, M. I. and Jones, D. T.",
title = {{pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination}},
journal = "Bioinformatics",
year = "2009",
volume = "25",
pages = "1761-1767",
month = "Jul",
pmid = "19429599",
}

@Article{Xu:2005,
author = "Xu, J.",
title = {Fold recognition by predicted alignment accuracy},
journal = "IEEE/ACM Trans Comput Biol Bioinform",
year = "2005",
volume = "2",
pages = "157-165",
month = "Apr-Jun",
pmid = "17044180",
}

@Article{Teichert:2010,
author = "Teichert, F. and Minning, J. and Bastolla, U. and Porto, M.",
title = {{High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH}},
journal = "BMC Bioinformatics",
year = "2010",
volume = "11",
pages = "251-251",
month = "",
pmid = "20470364",
}


@Article{Rice:1997,
author = "Rice, D. W. and Eisenberg, D.",
title = {{A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence}},
journal = "J. Mol. Biol.",
year = "1997",
volume = "267",
pages = "1026-1038",
month = "Apr",
pmid = "9135128",
}

@Article{Peng:2009,
author = "Peng, J. and Xu, J.",
title = {Boosting Protein Threading Accuracy},
journal = "Lect Notes Comput Sci",
year = "2009",
volume = "5541",
pages = "31-45",
month = "Jan",
pmid = "20169009",
}

@Article{Wu:2008,
author = "Wu, S. and Zhang, Y",
title = {{MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information}},
journal = "Proteins",
year = "2008",
volume = "72",
pages = "547-556",
month = "Aug",
pmid = "18247410",
}


@Article{Liu:2007,
author = "Liu, S. and Zhang, C. and Liang, S. and Zhou, Y",
title = {Fold recognition by concurrent use of solvent accessibility and residue depth},
journal = "Proteins",
year = "2007",
volume = "68",
pages = "636-645",
month = "Aug",
pmid = "17510969",
}

@article{Zhang2008,
  title={{SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model}},
  author={Zhang, W. and Liu, S. and Zhou, Y.},
  journal={PLoS One},
  volume={3},
  pages={2325},
  issn={1932-6203},
  year={2008},
  publisher={PLoS}
}



@Article{Karchin:2003,
author = "Karchin, R. and Cline, M. and Mandel-Gutfreund, Y. and Karplus, K.",
title = {{Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry}},
journal = "Proteins",
year = "2003",
volume = "51",
pages = "504-514",
month = "Jun",
pmid = "12784210",
}



@Article{Rost:1997,
author = "Rost, B. and Schneider, R. and Sander, C.",
title = {{Protein fold recognition by prediction-based threading}},
journal = "J. Mol. Biol.",
year = "1997",
volume = "270",
pages = "471-480",
month = "Jul",
pmid = "9237912",
}

@article{Madera:2008,
  title={{Profile Comparer: a program for scoring and aligning profile hidden Markov models}},
  author={Madera, M.},
  journal={Bioinformatics},
  volume={24},
  pages={2630},
  issn={1367-4803},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{Hildebrand:2009,
  title={{Fast and accurate automatic structure prediction with HHpred}},
  author={Hildebrand, A. and Remmert, M. and Biegert, A. and S\"oding, J.},
  journal={Proteins},
  volume={77},
  pages={128-132},
  issn={1097-0134},
  year={2009},
  publisher={John Wiley \& Sons}
}


@article{Karplus:2009,
  title={{SAM-T08, HMM-based protein structure prediction}},
  author={Karplus, K.},
  journal={Nucleic Acids Res.},
  volume={37},
  pages={W492-W497},
  year={2009},
  publisher={Oxford Univ Press}
}


@article{Eddy:2009,
  title={{A new generation of homology search tools based on probabilistic inference}},
  author={Eddy, S.R.},
  journal={Genome Inform.},
  volume={23},
  pages={205-211},
  year={2009},
}

@article{Cozzetto:2009,
  title={{Evaluation of template-based models in CASP8 with standard measures}},
  author={Cozzetto, D. and Kryshtafovych, A. and Fidelis, K. and Moult, J. and Rost, B. and Tramontano, A.},
  journal={Proteins},
  volume={77},
  pages={18-28},
  issn={1097-0134},
  year={2009},
  publisher={John Wiley \& Sons}
}

@article{Xu:2009,
  title={{Computational methods for protein sequence comparison and search}},
  author={Xu, D.},
  journal={Curr Protoc Prot Sci},
  volume={56},
  pages={2.1.1-2.1.27},
  year={2009},
  publisher={Wiley Interscience}
}

@article{Dunbrack:2006,
  title={{Sequence comparison and protein structure prediction}},
  author={Dunbrack, R. L.},
  journal={Curr. Opin. Struct. Biol.},
  volume={16},
  pages={374-384},
  issn={0959-440X},
  year={2006},
  publisher={Elsevier}
}

@article{Marchler:2011,
  title={{CDD: a Conserved Domain Database for the functional annotation of proteins}},
  author = "Marchler-Bauer, A. and Lu, S. and Anderson, J. B. and Chitsaz, F. and Derbyshire, M. K. and DeWeese-Scott, C. and Fong, J. H. and Geer, L. Y. and Geer, R. C. and Gonzales, N. R. and Gwadz, M. and Hurwitz, D. I. and Jackson, J. D. and Ke, Z. and Lanczycki, C. J. and Lu, F. and Marchler, G. H. and Mullokandov, M. and Omelchenko, M. V. and Robertson, C. L. and Song, J. S. and Thanki, N. and Yamashita, R. A. and Zhang, D. and Zhang, N. and Zheng, C. and Bryant, S. H.",
  journal={Nucleic Acids Res.},
  volume={39},
 pages={D225-229},
  issn={0305-1048},
  year={2011},
  publisher={Oxford Univ Press}
}

@article{Hunter:2009,
  title={{InterPro: the integrative protein signature database}},
  author = "Hunter, S. and Apweiler, R. and Attwood, T. K. and Bairoch, A. and Bateman, A. and Binns, D. and Bork, P. and Das, U. and Daugherty, L. and Duquenne, L. and Finn, R. D. and Gough, J. and Haft, D. and Hulo, N. and Kahn, D. and Kelly, E. and Laugraud, A. and Letunic, I. and Lonsdale, D. and Lopez, R. and Madera, M. and Maslen, J. and McAnulla, C. and McDowall, J. and Mistry, J. and Mitchell, A. and Mulder, N. and Natale, D. and Orengo, C. and Quinn, A. F. and Selengut, J. D. and Sigrist, C. J. and Thimma, M. and Thomas, P. D. and Valentin, F. and Wilson, D. and Wu, C. H. and Yeats, C.",
  journal={Nucleic Acids Res.},
  volume={37},
  pages={D211-205},
  issn={0305-1048},
  year={2009},
  publisher={Oxford Univ Press}
}

@article{Finn:2010,
  title={{The Pfam protein families database}},
  author={Finn, R. D. and Mistry, J. and Tate, J. and Coggill, P. and Heger, A. and Pollington, J.E. and Gavin, O. L. and Gunasekaran, P. and Ceric, G. and Forslund, K. and Holm, L. and Sonnhammer, E. L. and Eddy, S. R. and Bateman A.},
  journal={Nucleic Acids Res.},
  volume={38},
  pages={D211-222},
  year={2010},
  publisher={Oxford Univ Press}
}

@article{Murzin:1998,
author = "Murzin, A. G.",
title = {How far divergent evolution goes in proteins},
journal = "Curr. Opin. Struct. Biol.",
year = "1998",
volume = "8",
pages = "380-387",
month = "Jun",
pmid = "9666335",
}


@article{Alva:2008,
  title={{Cradle-loop barrels and the concept of metafolds in protein classification by natural descent}},
  author={Alva, V. and Koretke, K. K. and Coles, M. and Lupas, A. N.},
  journal={Curr. Opin. Struct. Biol.},
  volume={18},
  pages={358-365},
  issn={0959-440X},
  year={2008},
  publisher={Elsevier}
}

@Article{Kamada:2003,
   Author="Kamada, K. and Hanaoka, F. and Burley, Stephen K.",
   Title="{Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition}",
   Journal="Mol Cell",
   Year="2003",
   Volume="11",
   Pages="875-884",
}

@Article{O'Reilly:1997,
   Author="O'Reilly, M. and Devine, K. M.",
   Title="{Expression of AbrB, a transition state regulator from Bacillus subtilis, is growth phase dependent in a manner resembling that of Fis, the nucleoid binding protein from Escherichia coli}",
   Journal="J. Bacteriol",
   Year="1997",
   Volume="179",
   Pages="522-529",
}

@Article{Bagyan:1996,
   Author="Bagyan, I. and Hobot, J. and Cutting, S.",
   Title="{A compartmentalized regulator of developmental gene expression in Bacillus subtilis}",
   Journal="J. Bacteriol",
   Year="1996",
   Volume="178",
   Pages="4500-4507",
}

@Article{Venclovas:2000,
   Author="Venclovas, C. and Thelen, M. P.",
   Title="{Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes}",
   Journal="Nucleic Acids Res.",
   Year="2000",
   Volume="28",
   Pages="2481-2493",
}

@Article{Sali:1993,
   Author="Sali, A. and Blundell, T. L.",
   Title="{Comparative protein modelling by satisfaction of spatial restraints}",
   Journal="J. Mol. Biol.",
   Year="1993",
   Volume="234",
   Pages="779-815",
}

@Article{Dong:2004,
   Author="Dong, Tran Cat and Cutting, Simon M and Lewis, Richard J",
   Title="{DNA-binding studies on the Bacillus subtilis transcriptional regulator and AbrB homologue, SpoVT}",
   Journal="FEMS Microbiol Lett",
   Year="2004",
   Volume="233",
   Pages="247-256",
 }

@Article{Kihara:2004,
   Author="Kihara, D. and Skolnick, J.",
   Title="{Microbial genomes have over 72\% structure assignment by the threading algorithm PROSPECTOR\_Q}",
   Journal="Proteins",
   Year="2004",
   Volume="55",
   Pages="464-473",
}

% 9711271 (JID)
@Article{Pawlowski:2000,
   Author="Pawlowski, K. and Jaroszewski, L. and Rychlewski, L. and Godzik, A.",
   Title="{Sensitive sequence comparison as protein function predictor}",
   Journal="Pac Symp Biocomput",
   Year="2000",
   Pages="42-53"
}

% 9604387 (JID) 
@Article{Rychlewski:1998,
Author="Rychlewski, L. and Zhang, B. and Godzik, A.", 
Title="{Fold and function predictions for Mycoplasma genitalium proteins}", 
Journal="Fold Des", 
Year="1998", 
Volume="3", 
Pages="229-238" 
}

% 9211750 (JID) 
@Article{Rychlewski:1999, 
Author="Rychlewski, L. and Zhang, B. and Godzik, A.",
Title="{Functional insights from structural predictions: analysis of the Escherichia coli genome}",
Journal="Protein Sci", 
Year="1999", 
Volume="8", 
Pages="614-624", 
}

@Article{Pawlak:2005,
Author="Pawlak, S. D. and Radlinska, M. and Chmiel, A. A. and Bujnicki, J. M. and Skowronek, K. J.",
Title="{Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII}",
Journal="Nucleic Acids Res.",
Year="2005",
Volume="33",
Pages="661-671"
}

@Article{Rand:2004,
Author={Rand, T. A. and Ginalski, K. and Grishin, N. V. and Wang, X.},
Title="{Biochemical identification of Argonaute 2 as the sole protein required for {RNA}-induced silencing complex activity}",
Journal={Proc. Natl. Acad. Sci. USA},
Year={2004},
Volume={101},
Pages={14385-14389},
}


@Article{Zheng:2005,
Author={Zheng, M. and Ginalski, K. and Rychlewski, L. and Grishin, N. V.}, 
Title="{Protein domain of unknown function {DUF1023} is an alpha/beta hydrolase}", 
Journal={Proteins}, 
Year={2005}, 
Volume = {6},
Pages ={1-6}
}

% 0411011 (JID) 
@Article{Ginalski:2004a, 
Author={Ginalski, K. and von Grotthuss, M. and Grishin, Nick V. and Rychlewski, L.}, 
Title="{Detecting distant homology with Meta-BASIC}", 
Journal={Nucleic Acids Res.}, 
Year={2004}, 
Volume={32}, 
Pages={W576-581}, 
}

% 7505876 (JID) 
@Article{Ginalski:2004b, 
Author={Ginalski, K. and Rychlewski, L. and Baker, D. and Grishin, N. V.}, 
Title="{Protein structure prediction for the male-specific region of the human Y chromosome}", 
Journal={Proc Natl Acad Sci USA}, 
Year={2004}, 
Volume={101}, 
Pages={2305-2310}, 
} 

@ARTICLE{Soding:2005,
AUTHOR  = {S\"oding, J.},
TITLE   = {{Protein homology detection by HMM-HMM comparison}},
YEAR    = {2005},
JOURNAL = {Bioinformatics},
VOLUME  = {21},
PAGES   = {951-960}
}

@ARTICLE{Todd:2002,
AUTHOR  = {Todd, A.E. and Orengo, C.A. and Thornton, J.M.},
TITLE   = {Plasticity of enzyme active sites},
YEAR    = {2002},
JOURNAL  = {Trends Biochem Sci.},
VOLUME  = {27},
PAGES   = {419-426}
}

@Article{COG:2003,
author = {Tatusov, R. L. and Fedorova, N. D. and Jackson, J. D. and Jacobs, A. R. and Kiryutin, B. and Koonin, E. V. and Krylov, D. M. and Mazumder, R. and Mekhedov, S. L. and Nikolskaya, A. N. and Rao, B. S. and Smirnov, S. and Sverdlov, A. V. and Vasudevan, S. and Wolf, Y. I. and Yin, J. J. and Natale, D. A.},
title = {The {COG} database: an updated version includes eukaryotes},
journal = {BMC Bioinformatics},
year = {2003},
volume = {4},
pages = {41-41},
pmid = {12969510},
url = "{http://www.hubmed.org/display.cgi?uids=12969510}"
}

@Article{SMART:1999,
author = "Ponting, C. P. and Schultz, J. and Milpetz, F. and Bork, P.",
title = "{SMART: identification and annotation of domains from signalling and extracellular protein sequences}",
journal = "Nucleic Acids Res.",
year = "1999",
volume = "27",
pages = "229-232",
pmid = "9847187",
url = "{http://www.hubmed.org/display.cgi?uids=9847187}"
}

@Article{Pfam:1998,
author = "Sonnhammer, E. L. and Eddy, S. R. and Birney, E. and Bateman, A. and Durbin, R.",
title = "{Pfam: multiple sequence alignments and HMM-profiles of protein domains}",
journal = "Nucleic Acids Res.",
year = "1998",
volume = "26",
pages = "320-322",
pmid = "9399864",
}

@ARTICLE{CDD:2002,
AUTHOR  = {Marchler-Bauer, A. and Panchenko, A.R. and Shoemaker, B. A. and Thiessen, P. A. and Geer, L.Y. and Bryant, S.H.},
TITLE   = {{CDD}: a database of conserved domain alignments with links to domain three-dimensional structure},
YEAR    = {2002},
JOURNAL  = {Nucleic Acids Res.},
VOLUME  = {30},
PAGES   = {D281-283}
}

@ARTICLE{SCOP:2000,
AUTHOR  = {Lo Conte, L. and Ailey, B. and Hubbard, T. J. and Brenner, S. E. and Murzin, A. G. and Chothia, C.},
TITLE   = {{SCOP}: a structural classification of proteins database},
YEAR    = {2000},
JOURNAL  = { Nucleic Acids Res.},
VOLUME  = {28},
PAGES   = {257-259}
}

@ARTICLE{PDB:2004,
AUTHOR  = {Bourne, P .E. and Addess, K. J. and Bluhm, W. F. and Chen, L. and Deshpande, N. and Feng, Z. and Fleri, W. and Green, R. and Merino-Ott, J. C. and Townsend-Merino, W. and Weissig, H. and Westbrook, J. and Berman, H. M.},
TITLE   = {The distribution and query systems of the {RCSB} Protein Data Bank},
YEAR    = {2004},
JOURNAL  = {Nucleic Acid Res.},
VOLUME  = {32},
PAGES   = {D223-225}
}


@ARTICLE{Bork:1998,
AUTHOR  = {Bork, P. and Koonin, E. V.},
TITLE   = {Predicting functions from protein sequences -- where are the bottlenecks},
YEAR    = {1998},
JOURNAL  = {Nat. Genet.},
VOLUME  = {18},
PAGES   = {313-318}
}

@ARTICLE{Kinch:2003,
AUTHOR  = {Kinch, L. N. and Wrabl, J. O. and Krishna, S. S. and Majumdar, I. and Sadreyev, R. I. and Qi, Y. and Pei, J. and Cheng H. and Grishin, N. V.},
TITLE   = {{CASP}5 assessment of fold recognition target predictions},
YEAR    = {2003},
JOURNAL  = {Proteins},
VOLUME  = {53},
PAGES   = {395-409}
}

@ARTICLE{Todd:2001,
AUTHOR  = {Todd, A. E. and Orengo, C. A. and Thornton, J. M.},
TITLE   = {Evolution of function in protein superfamilies, from a structural perspective},
YEAR    = {2001},
JOURNAL  = {J. Mol. Biol.},
VOLUME  = {307},
PAGES   = {1113-1143}
}

@ARTICLE{Henn-Sax:2001,
AUTHOR  = {Henn-Sax, M. and Hocker B. and Wilmanns, M. and Sterner, R.},
TITLE   = {Divergent evolution of $(\beta \alpha)_8$--barrel enzymes},
YEAR    = {2001},
JOURNAL  = {Biol. Chem.},
VOLUME  = {382},
PAGES   = {1315-1320}
}

@ARTICLE{Frickey:2004,
AUTHOR  = {Frickey, T. and Lupas, A. N.},
TITLE   = {Phylogenetic analysis of {AAA} proteins},
YEAR    = {2004},
JOURNAL  = {J. Struct. Biol.},
VOLUME  = {146},
PAGES   = {2-10}
}

@Article{Altschul:1990,
   Author="Altschul, S F. and Gish, W and Miller, W and Myers, E W and Lipman, D. J",
   Title="{Basic local alignment search tool}",
   Journal="J. Mol. Biol.",
   Year="1990",
   Volume="215",
   Pages="403-410",
}

@ARTICLE{Altschul:1997,
AUTHOR  = {Altschul, S. F. and Madden, T. L. and Sch\"affer, A. A. and Zhang, J. and Zhang, Zh. and Miller, W. and Lipman, D.},
TITLE   = {Gapped {BLAST} and {PSI-BLAST}: a new generation of protein database search programs},
YEAR    = {1997},
JOURNAL  = {Nucleic Acids Res.},
VOLUME  = {25},
PAGES   = {3389-3402}
}


@ARTICLE{Pearson:1991,
AUTHOR  = {Pearson, W. R.},
TITLE   = "{Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and {FASTA} algorithms}",
YEAR    = {1991},
JOURNAL  = {Genomics},
VOLUME  = {11},
PAGES   = {635-650}
}

@ARTICLE{Pearson:2000,
AUTHOR  = {Pearson, W. R.},
TITLE   = {Flexible sequence similarity searching with the {FASTA}3 program package},
YEAR    = {2000},
JOURNAL  = {Methods Mol. Biol.},
VOLUME  = {132},
PAGES   = {185-219}
}

@ARTICLE{LAMA,
AUTHOR  = {Pietrokovski, S.},
TITLE   = {Searching databases of conserved sequence regions by aligning protein multiple-alignments},
YEAR    = {1996},
JOURNAL  = {Nucleic Acids Res.},
VOLUME  = {24},
PAGES   = {3836-3845}
}

@ARTICLE{Yona:2002,
AUTHOR  = {Yona, G. and Levitt, M.},
TITLE   = {Within the twilight zone: a sensitive profile--profile comparison tool based on information theory},
YEAR    = {2002},
JOURNAL  = {J. Mol. Biol.},
VOLUME  = {315},
PAGES   = {1257-1275}
}

@ARTICLE{Sadreyev:2003,
AUTHOR  = {Sadreyev, R. I. and Grishin, N. V.},
TITLE   = {{COMPASS}: A tool for comparison of multiple protein alignments with assessment of statistical significance},
YEAR    = {2003},
JOURNAL  = {J. Mol. Biol.},
VOLUME  = {326},
PAGES   = {317-336}
}

@ARTICLE{Sadreyev:2003b,
AUTHOR  = {Sadreyev, R. I. and Baker, D. and Grishin, N. V.},
TITLE   = {Profile--profile comparisons by {COMPASS} predict intricate homologies between protein families},
YEAR    = {2003},
JOURNAL  = {Protein Sci.},
VOLUME  = {12},
PAGES   = {2262-2272}
}

@ARTICLE{CYCRA,
AUTHOR  = {Kunin, V. and Chan, B. and Sitbon, E. and Lithwick, G. and Pietrokovski, S.},
TITLE   = {Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs},
YEAR    = {2001},
JOURNAL  = {J. Mol. Biol.},
VOLUME  = {307},
PAGES   = {939-949}
}

@ARTICLE{Thompson:1994,
AUTHOR  = {Thompson, J. D. and Higgins, D. G. and Gibson, T. J.},
TITLE   = {{CLUSTAL W}: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice},
YEAR    = {1994},
JOURNAL  = {Nucleic Acids Res.},
VOLUME  = {22},
PAGES   = {4673-4680}
}

@ARTICLE{PCMA,
AUTHOR  = {Pei, J. and Sadreyev, R. and Grishin, N. V.},
TITLE   = {{PCMA}: fast and accurate multiple sequence alignment based on profile consistency},
YEAR    = {2003},
JOURNAL  = {Bioinformatics},
VOLUME  = {19},
PAGES   = {427-428}
}

@ARTICLE{SATCHMO,
AUTHOR  = {Edgar, R. C. and Sj\"olander, K.},
TITLE   = {{SATCHMO}: sequence alignment and tree construction using hidden Markov models},
YEAR    = {2003},
JOURNAL  = {Bioinformatics},
VOLUME  = {19},
PAGES   = {1404-1411}
}

@ARTICLE{Kinch:2002,
AUTHOR  = {Kinch, L.N. and Grishin, N.V.},
TITLE   = {Evolution of protein structures and functions},
YEAR    = {2002},
JOURNAL  = {Curr. Opin. Struct. Biol.},
VOLUME  = {12},
PAGES   = {400-408}
}

@ARTICLE{Rychlewski:2000,
AUTHOR  = {Rychlewski, L. and Jaroszewski, L. and Li, W. and Godzik, A.},
TITLE   = {Comparison of sequence-profiles. Strategies for structural predictions using sequence information},
YEAR    = {2000},
JOURNAL  = {Protein Science},
VOLUME  = {9},
PAGES   = {232-241}
}


@ARTICLE{Ginalski:2003,
AUTHOR  = {Ginalski, K. and Pas, J. and Wyrwicz, L. S. and von Grotthus, M. and Bujnicki, J. M. and Rychlewski, L.},
TITLE   = {{ORF}eus: detection of distant homology using sequence profiles and predicted secondary structure},
YEAR    = {2003},
JOURNAL  = {Nucleic Acid Research},
VOLUME  = {31},
PAGES   = {3804-3807}
}

@ARTICLE{Ginalski:2003b,
AUTHOR  = {Ginalski, K. and Elofsson, A. and Fischer, D. and Rychlewski, L.},
TITLE   = {{3D-Jury}: a simple approach to improve protein structure predictions},
YEAR    = {2003},
JOURNAL  = {Bioinformatics},
VOLUME  = {19},
PAGES   = {1015-1018}
}

@ARTICLE{Tang:2003,
AUTHOR  = {Tang, C. L. and Xie, L. and Koh, I. Y. and Posy, S. and Alexov, E. and Honig, B.},
TITLE   = {On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles},
YEAR    = {2003},
JOURNAL  = {J. Mol. Biol.},
VOLUME  = {334},
PAGES   = {1043-1062}
}

@ARTICLE{Ohsen:2003,
AUTHOR  = {von~\"{O}hsen, N. and Sommer, I. and Zimmer, R.},
TITLE   = {Profile--profile alignment: a powerful tool for protein structure prediction},
YEAR    = {2003}, 
JOURNAL = {Pac. Symp. Biocomput.},
PAGES   ={252-263}
}

@ARTICLE{Sommer:2002,
AUTHOR  = {Sommer, I. and Zien. and A. and von \"Ohsen, N. and Zimmer, R. and Lengauer, T.},
TITLE   = {Confidence measures for protein fold recognition},
YEAR    = {2002},
JOURNAL  = {Bioinformatics},
VOLUME  = {18},
PAGES   = {802-812}
}

@ARTICLE{FORTE:2004,
AUTHOR  = {Tomii, K. and Akiyama, Y.},
TITLE   = {{FORTE}: a profile--profile comparison tool for protein fold recognition},
YEAR    = {2004},
JOURNAL  = {Bioinformatics},
VOLUME  = {20},
PAGES   = {594-595}
}

@ARTICLE{Fischer:2003,
AUTHOR  = {Fischer, D.},
TITLE   = {{3D-SHOTGUN}: a novel, cooperative, fold-recognition meta-predictor},
YEAR    = {2003},
JOURNAL  = {Proteins},
VOLUME  = {51},
PAGES   = {434-441}
}

@ARTICLE{CAFASP:2003,
AUTHOR  = {Fischer, D. and Rychlewski, L. and Dunbrack, R. L. Jr and Ortiz, A. R. and Elofsson, A.},
TITLE   = "{CAFASP3: the third critical assessment of fully automated structure prediction methods}",
YEAR    = {2003},
JOURNAL  = {Proteins},
VOLUME  = {53},
PAGES   = {503-516}
}

@ARTICLE{LiveBench:2003,
AUTHOR  = {Rychlewski, L. and Fischer, D. and Elofsson, A.},
TITLE   = {{LiveBench}--6: large-scale automated evaluation of protein structure prediction servers},
YEAR    = {2003},
JOURNAL  = {Proteins},
VOLUME  = {53},
PAGES   = {542-547}
}

@ARTICLE{EVA,
AUTHOR  = {Koh, I.Y. and Eyrich, V. A. and Marti-Renom, M. A. and Przybylski, D. and Madhusudhan, M. S. and Eswar, N. and Grana, O. and Pazos, F. and Valencia, A. and Sali, A. and Rost, B.},
TITLE   = {{EVA}: Evaluation of protein structure prediction servers},
YEAR    = {2003},
JOURNAL  = {Nucleic Acids Res.},
VOLUME  = {31},
PAGES   = {3311-3315}
}

@BOOK{Durbin:2008,
AUTHOR  = {Durbin, R. and Eddy, S. and Krogh, A. and Mitchison, G.},
TITLE   = {Biological sequence analysis: Probabilistic models of proteins and nucleic acids},
YEAR    = {2008},
PUBLISHER = {Cambridge Univ. Press, Cambridge}
}

@BOOK{Durbin:1998,
AUTHOR  = {Durbin, R. and Eddy, S. and Krogh, A. and Mitchison, G.},
TITLE   = {Biological sequence analysis: Probabilistic models of proteins and nucleic acids},
YEAR    = {1998},
PUBLISHER = {Cambridge University Press, Cambridge}
}

@ARTICLE{Krogh:1994,
AUTHOR  = {Krogh, A. and Brown, M. and Mian, I. S. and Sj\"olander, K. and Haussler, D.},
TITLE   = {Hidden Markov models in computational biology. {A}pplications to protein modeling},
YEAR    = {1994},
JOURNAL  = {J. Mol. Biol.},
VOLUME  = {235},
PAGES   = {1501-1531}
}

@ARTICLE{Bucher:1996,
AUTHOR  = {Bucher, P. and Karplus, K. and Moeri, N. and Hofmann, K.},
TITLE   = {A flexible motif search technique based on generalized profiles},
YEAR    = {1996},
JOURNAL  = {Comput. Chem.},
VOLUME  = {20},
PAGES   = {3-23}
}

@ARTICLE{Eddy:1998,
AUTHOR  = {Eddy, S. R.},
TITLE   = {Profile hidden Markov models},
YEAR    = {1998},
JOURNAL  = {Bioinformatics},
VOLUME  = {14},
PAGES   = {755-763}
}

@ARTICLE{Karplus:2001,
AUTHOR  = {Karplus, K. and Karchin, R. and Barrett, C. and Tu, S. and Cline, M. and Diekhans, M. and Grate, L. and Casper, J. and Hughey, R.},
TITLE   = {What is the value added by human intervention in protein structure prediction},
YEAR    = {2001},
JOURNAL  = {Proteins},
VOLUME  = {45},
ISSUE   = {Suppl. 5},
PAGES   = {86-91}
}

@article{Karplus:1998,
  title={{Hidden Markov models for detecting remote protein homologies.}},
  author={Karplus, K. and Barrett, C. and Hughey, R.},
  journal={Bioinformatics},
  volume={14},
  pages={846-856},
  year={1998},
}

@ARTICLE{META-MEME,
AUTHOR  = {Grundy, W.N. and Bailey, T.L. and Elkan, C.P. and Baker, M. E.},
TITLE   = {Meta-{MEME}: motif-based hidden Markov models of protein families},
YEAR    = {1997},
JOURNAL  = {Comput. Appl. Biosci.},
VOLUME  = {13},
PAGES   = {397-406}
}

@ARTICLE{Lyngso:1999,
AUTHOR  = {Lyngs{\o}, R. B. and Pedersen, C. N. S. and Nielsen, H.},
TITLE   = {Metrics and similarity measures for hidden Markov models},
YEAR    = {1999},
JOURNAL = {Proc. Int. Conf. Intell. Syst. Mol. Biol.},
PAGES   = {178-186}
}

@ARTICLE{3D-PSSM,
AUTHOR  = {Kelley, L. A. and MacCallum, R. M. and Sternberg, M. J.},
TITLE   = {Enhanced genome annotation using structural profiles in the program {3D-PSSM}},
YEAR    = {2000},
JOURNAL  = {J. Mol. Biol.},
VOLUME  = {299},
PAGES   = {499-520}
}

@ARTICLE{Grigoriev:2001,
AUTHOR  = {Grigoriev, I. V. and Zhang, C. and Kim, S. H.},
TITLE   = {Sequence-based detection of distantly related proteins with the same fold},
YEAR    = {2001},
JOURNAL  = {Protein Eng.},
VOLUME  = {14},
PAGES   = {455-458}
}

@ARTICLE{Hargbo:1999,
AUTHOR  = {Hargbo, J. and Elofsson, A.},
TITLE   = {Hidden Markov models that use predicted secondary structures for fold recognition},
YEAR    = {1999},
JOURNAL  = {Proteins},
VOLUME  = {36},
PAGES   = {68-76}
}

@ARTICLE{Jones:1999,
AUTHOR  = {Jones, D. T.},
TITLE   = {Protein secondary structure prediction based on position-specific scoring matrices},
YEAR    = {1999},
JOURNAL  = {J. Mol. Biol.},
VOLUME  = {292},
PAGES   = {195-202}
}

@ARTICLE{Kawabata:2000,
AUTHOR  = {Kawabata, T. and Nishikawa, K.},
TITLE   = {Protein structure comparison using the markov transition model of evolution},
YEAR    = {2000},
JOURNAL  = {Proteins},
VOLUME  = {41},
PAGES   = {108-122}
}

@ARTICLE{Kabsch:1983,
AUTHOR  = {Kabsch, W. and Sander, C.},
TITLE   = {Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features},
YEAR    = {1983},
JOURNAL  = {Biopolymers},
VOLUME  = {22},
PAGES   = {2577-2637}
}

@ARTICLE{BLOCKS,
AUTHOR  = {Henikoff, S. and Henikoff, J. G.},
TITLE   = {Protein family classification based on searching a database of blocks},
YEAR    = {1994},
JOURNAL  = {Genomics},
VOLUME  = {19},
PAGES   = {97-107}
}

@ARTICLE{MAST,
AUTHOR  = {Bailey, T. L. and Gribskov, M.},
TITLE   = {Methods and statistics for combining motif match scores},
YEAR    = {1998},
JOURNAL  = {J. Comput. Biol.},
VOLUME  = {5},
PAGES   = {211-221}
}

@ARTICLE{Wang:2004,
AUTHOR  = {Wang, G. and Dunbrack, R. L. Jr.},
TITLE   = {Scoring profile--profile sequence alignments},
YEAR    = {2004},
JOURNAL  = {Protein Sci.},
VOLUME  = {13},
PAGES   = {1612-1626}
}

@ARTICLE{Barrett:1997,
AUTHOR  = {Barrett, C. and Hughey, R. and Karplus, K.},
TITLE   = {Scoring hidden Markov models},
YEAR    = {1997},
JOURNAL  = {Comput. Appl. Biosci.},
VOLUME  = {13},
PAGES   = {191-199}
}

@ARTICLE{Henikoff:1994,
AUTHOR  = {Henikoff, S. and Henikoff, J. G.},
TITLE   = {Position-based sequence weights},
YEAR    = {1994},
JOURNAL  = {J. Mol. Biol.},
VOLUME  = {243},
PAGES   = {574-578}
}

@ARTICLE{Gonnet:1992,
AUTHOR  = {Gonnet, G. H. and Cohen, M. A. and Brenner, S. A.},
TITLE   = {Exhaustive matching of the entire protein sequence database},
YEAR    = {1992},
JOURNAL  = {Science},
VOLUME  = {256},
PAGES   = {1443-1445}
}

@ARTICLE{Fischer:1996,
AUTHOR  = {Fischer, D. and Elofsson, A. and Rice, D. and Eisenberg, D.},
TITLE   = {Assessing the performance of fold recognition methods by means of a comprehensive benchmark},
YEAR    = {1996},
JOURNAL = {Pac. Symp. Biocomput. 1996},
PAGES   = {300-318}
}

@ARTICLE{Pei:2001,
AUTHOR  = {Pei, J. and Grishin, N. V.},
TITLE   = {{AL2CO}: calculation of positional conservation in a protein sequence alignment},
YEAR    = {2001},
JOURNAL  = {Bioinformatics},
VOLUME  = {17},
PAGES   = {700-712}
}

@BOOK{Hastie:2001,
AUTHOR  = {Hastie, T. and Tibshirani, R. and Friedman, J.},
TITLE   = {The Elements of Statistical Learning},
PUBLISHER ={Springer},
SERIES  = {Springer series in statistics}, 
YEAR    = {2001}
}

@ARTICLE{Pearson:1995,
AUTHOR  = {Pearson, W. R.},
TITLE   = {Comparison of methods for searching protein sequence databases},
YEAR    = {1995},
JOURNAL  = {Protein Sci.},
VOLUME  = {4},
PAGES   = {1145-1160}
}

@ARTICLE{twilight,
AUTHOR  = {Doolittle, R. F.},
TITLE   = {Similar amino acid sequences: chance or common ancestry},
YEAR    = {1981},
JOURNAL  = {Science},
VOLUME  = {214},
PAGES   = {149-159}
}

@ARTICLE{Andreeva:2004,
AUTHOR  = {Andreeva, A. and Howorth, D. and Brenner, S. E. and Hubbard, T. J. and Chothia, C. and Murzin, A. G.},
TITLE   = {{SCOP} database in 2004: refinements integrate structure and sequence family data},
YEAR    = {2004},
JOURNAL  = {Nucleic Acids Res.},
VOLUME  = {32},
PAGES   = {D226-229}
}

@ARTICLE{Murzin:1995,
AUTHOR  = {Murzin, A. G. and Brenner, S. E. and Hubbard, T. and Chothia, C.},
TITLE   = {{SCOP}: a structural classification of proteins database for the investigation of sequences and structures},
YEAR    = {1995},
JOURNAL  = {J. Mol. Biol.},
VOLUME  = {247},
PAGES   = {536-540}
}

@ARTICLE{Mittelman:2003,
AUTHOR  = {Mittelman, D. and Sadreyev, R. and Grishin, N. V.},
TITLE   = {Probabilistic scoring measures for profile--profile comparison yields more accurate short seed alignments},
YEAR    = {2003},
JOURNAL  = {Bioinformatics},
VOLUME  = {19},
PAGES   = {1531-1539}
}

@ARTICLE{Panchenko:2003,
AUTHOR  = {Panchenko, A. R.},
TITLE   = {Finding weak similarities between proteins by sequence profile comparison},
YEAR    = {2003},
JOURNAL  = {Nucleic Acids Res.},
VOLUME  = {31},
PAGES   = {683-689}
}

@ARTICLE{Marti-Renom:2004,
AUTHOR  = {Marti-Renom, M. A. and Madhusudhan, M. S. and Sali, A.},
TITLE   = {Alignment of protein sequences by their profiles},
YEAR    = {2004},
JOURNAL  = {Protein Sci.},
VOLUME  = {13},
PAGES   = {1071-87}
}

@ARTICLE{Edgar:2004,
AUTHOR  = {Edgar, R. C. and Sj\"olander, K.},
TITLE   = {A comparison of scoring functions for protein sequence profile alignment},
YEAR    = {2004},
JOURNAL  = {Bioinformatics},
VOLUME  = {20},
PAGES   = {1301-1308}
}

@ARTICLE{Chandonia:2004,
AUTHOR  = {Chandonia, J. M. and Hon, G. and Walker, N. S. and Lo Conte, L. and Koehl, P. and Levitt, M. and Brenner, S.E.},
TITLE   = {The {ASTRAL} compendium in 2004},
YEAR    = {2004},
JOURNAL  = {Nucleic Acids Research},
VOLUME  = {32},
PAGES   = {D189-D192}
}

@ARTICLE{Siew:2000,
AUTHOR  = {Siew, N. and Elofsson, A. and Rychlewski, L. and Fischer, D.},
TITLE   = {{MaxSub}: an automated measure for the assessment of protein structure prediction quality},
YEAR    = {2000},
JOURNAL  = {Bioinformatics},
VOLUME  = {16},
PAGES   = {776-85}
}

@ARTICLE{O'Sullivan:2003,
AUTHOR  = {O'Sullivan, Orla and Zehnder, Marc and Higgins, Des and Bucher, Philipp and Grosdidier, Aurelien and Notredame, Cédric},
TITLE   = {{APDB}: a novel measure for benchmarking sequence alignment methods without reference alignments},
YEAR    = {2003},
JOURNAL  = {Bioinformatics},
VOLUME  = {19},
PAGES   = {i215-i221}
}

@ARTICLE{Venclovas:2003,
AUTHOR  = {Venclovas, C.},
TITLE   = {Comparative modeling in {CASP}5: progress is evident, but alignment errors remain a significant hindrance},
YEAR    = {2003},
JOURNAL = {Proteins},
VOLUME  = {53},
PAGES   = {380-388}
}

@ARTICLE{Cline:2002,
AUTHOR  = {Cline, M. and Hughey, R. and Karplus, K.},
TITLE   = {Predicting reliable regions in protein sequence alignments},
YEAR    = {2002},
JOURNAL = {Bioinformatics},
VOLUME  = {18},
PAGES   = {306-314}
}

@ARTICLE{Sauder:2000,
AUTHOR  = {Sauder, J. M. and Arthur, J. W. and Dunbrack, R. L. Jr.},
TITLE   = {Large-scale comparison of protein sequence alignment algorithms with structure alignments},
YEAR    = {2000},
JOURNAL = {Proteins},
VOLUME  = {40},
PAGES   = {6-22}
}

@ARTICLE{Pruitt:2003,
AUTHOR  = {Pruitt, K.D. and Tatusova, T. and Maglott, D.R.},
TITLE   = {{NCBI} Reference Sequence project: update and current status},
YEAR    = {2003},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {31},
PAGES   = {34-37}
}

@ARTICLE{Li:2002a,
AUTHOR  = {Li, W. and Jaroszewski, L. and Godzik, A.},
TITLE   = {Tolerating some redundancy significantly speeds up clustering of large protein databases},
YEAR    = {2002},
JOURNAL = {Bioinformatics},
VOLUME  = {18},
PAGES   = {77-82}
}

@ARTICLE{Li:2002b,
AUTHOR  = {Li, W. and Jaroszewski, L. and Godzik, A.},
TITLE   = {Sequence clustering strategies improve remote homology recognitions while reducing search times},
YEAR    = {2002},
JOURNAL = {Protein Eng.},
VOLUME  = {15},
PAGES   = {643-649}
}

@ARTICLE{FASTA,
AUTHOR  = {Pearson, W. R. and Lipman, D. J.},
TITLE   = {Improved tools for biological sequence comparison},
YEAR    = {1988},
JOURNAL = {Proc. Natl. Acad. Sci. USA},
VOLUME  = {85},
PAGES   = {2444-2448}
}


@ARTICLE{Pellegrini:1999,
AUTHOR  = {Pellegrini, M. and Marcotte, E. M. and Yeates, T. O.},
TITLE   = {A fast algorithm for genome-wide analysis of proteins with repeated sequences},
YEAR    = {1999},
JOURNAL = {Proteins},
VOLUME  = {35},
PAGES   = {440-446}
}

@ARTICLE{Taylor:2002,
AUTHOR  = {Taylor, W. R. and Heringa, J. and Baud, F. and Flores, T. P.},
TITLE   = {Fourier analysis of symmetry in protein structures},
YEAR    = {2002},
JOURNAL = {Prot. Eng.},
VOLUME  = {15},
PAGES   = {79-89}
}

@ARTICLE{Kajava:2001,
AUTHOR  = {Kajava, A. V.},
TITLE   = {Review: proteins with repeated sequence -- structural prediction and modeling},
YEAR    = {2001},
JOURNAL = {J. Struct. Biol.},
VOLUME  = {134},
PAGES   = {132-144}
}

@ARTICLE{Andrade:2001,
AUTHOR  = {Andrade, M. A. and Perez-Iratxeta, C. and Ponting, C. P.},
TITLE   = {Protein repeats: structures, functions, and evolution},
YEAR    = {2001},
JOURNAL = {J. Struct. Biol.},
VOLUME  = {134},
PAGES   = {117-131}
}

@ARTICLE{Mosavi:2004,
AUTHOR  = {Mosavi, L. K. and Cammett, T. J. and Desrosiers, D. C. and Peng, Z. Y.},
TITLE   = {The ankyrin repeat as molecular architecture for protein recognition},
YEAR    = {2004},
JOURNAL = {Protein. Sci.},
VOLUME  = {13},
PAGES   = {1435-1448}
}

@ARTICLE{vanNocker:2003,
AUTHOR  = {van Nocker, S. and Ludwig, P.},
TITLE   = {The {WD}-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function},
YEAR    = {2003},
JOURNAL = {BMC. Genomics.},
VOLUME  = {4},
PAGES   = {50}
}

@ARTICLE{Blatch:1999,
AUTHOR  = {Blatch, G. L. and Lassle, M.},
TITLE   = {The tetratricopeptide repeat: a structural motif mediating protein-protein interactions},
YEAR    = {1999},
JOURNAL = {Bioessays.},
VOLUME  = {21},
PAGES   = {932-939}
}

@ARTICLE{Cliff:2005,
AUTHOR  = {Cliff, M. J. and Williams, M. A. and Brooke-Smith, J. and Barford, D. and Ladbury, J. E.},
TITLE   = {Molecular recognition via coupled folding and binding in a TPR domain},
YEAR    = {2005},
JOURNAL = {J. Mol. Biol.},
VOLUME  = {346},
PAGES   = {717-732}
}

@ARTICLE{Graham:2002,
AUTHOR  = {Graham, T. A. and Clements, W. K. and Kimelman, D. and Xu, W.},
TITLE   = {The crystal structure of the beta-catenin/ICAT complex reveals the inhibitory mechanism of ICAT},
YEAR    = {2002},
JOURNAL = {Mol. Cell.},
VOLUME  = {10},
PAGES   = {563-571}
}

@ARTICLE{Graham:2001,
AUTHOR  = {Graham, T. A. and Ferkey, D. M. and Mao, F. and Kimelman, D. and Xu, W.},
TITLE   = {Tcf4 can specifically recognize beta-catenin using alternative conformations},
YEAR    = {2001},
JOURNAL = {Nat. Struct. Biol.},
VOLUME  = {8},
PAGES   = {1048-1052}
}

@ARTICLE{Dyson:2002,
AUTHOR  = {Dyson, H. J. and Wright, P. E.},
TITLE   = {Coupling of folding and binding for unstructured proteins},
YEAR    = {2002},
JOURNAL = {Curr. Opin. Struct. Biol.},
VOLUME  = {12},
PAGES   = {54-60}
}

@ARTICLE{REP:2000,
AUTHOR  = {Andrade, M. A. and Ponting, C. P. and Gibson, T. J. and Bork, P.},
TITLE   = {Homology-based method for identification of protein repeats using statistical significance estimates},
YEAR    = {2000},
JOURNAL = {J. Mol. Biol.},
VOLUME  = {298},
PAGES   = {521-537}
}

@ARTICLE{Heger:2000,
AUTHOR  = {Heger, A. and and Holm, L.},
TITLE   = {Rapid automatic detection and alignment of repeats in protein sequences},
YEAR    = {2000},
JOURNAL = {Proteins},
VOLUME  = {41},
PAGES   = {224-237}
}


@ARTICLE{TRUST:2004,
AUTHOR  = {Szklarczyk, R. and and Heringa, J.},
TITLE   = {Tracking repeats using significance and transitivity},
YEAR    = {2004},
JOURNAL = {Bioinformatics},
VOLUME  = {20},
PAGES   = {I311-I317}
}

@ARTICLE{REPRO:1993,
AUTHOR  = {Heringa, J. and Argos, P.},
TITLE   = {A method to recognize distant repeats in protein sequences},
YEAR    = {1993},
JOURNAL = {Proteins},
VOLUME  = {17},
PAGES   = {391-341}
}

@ARTICLE{Murray:2004,
AUTHOR  = {Murray, K. B. and Taylor, W. R. and Thornton, J. M.},
TITLE   = {Toward the detection and validation of repeats in protein structure},
YEAR    = {2004},
JOURNAL = {Proteins},
VOLUME  = {57},
PAGES   = {365-380}
}

@ARTICLE{Notredame:2000,
AUTHOR  = {Notredame, C. and Higgins, D. G. and Heringa, J.},
TITLE   = {T-Coffee: A novel method for fast and accurate multiple sequence alignment},
YEAR    = {2000},
JOURNAL = {J. Mol. Biol.},
VOLUME  = {302},
PAGES   = {205-217}
}

@ARTICLE{Gotoh:1990,
AUTHOR  = {Gotoh, O.},
TITLE   = {Consistency of optimal sequence alignments},
YEAR    = {1990},
JOURNAL = {Bull. Math. Biol.},
VOLUME  = {52},
PAGES   = {509-525}
}

@ARTICLE{Do:2005,
AUTHOR  = {Do, C. B. and Mahabhashyam, M. S. and Brudno, M. and Batzoglou, S.},
TITLE   = {ProbCons: Probabilistic consistency-based multiple sequence alignment},
YEAR    = {2005},
JOURNAL = {Genome. Res.},
VOLUME  = {15},
PAGES   = {330-340}
}

@ARTICLE{Sonnhammer:1995,
AUTHOR  = {Sonnhammer, E. L., and Durbin, R.},
TITLE   = {A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis},
YEAR    = {1995},
JOURNAL = {Gene},
VOLUME  = {167},
PAGES   = {GC1-10}
}

@ARTICLE{Soding:2003,
AUTHOR  = {S\"oding, J. and Lupas, A. N.},
TITLE   = {More than the sum of their parts: on the evolution of proteins from peptides},
YEAR    = {2003},
JOURNAL = {Bioessays},
VOLUME  = {25},
PAGES   = {837-846}
}

@ARTICLE{Soding:2006a,
AUTHOR  = {S\"oding, J. and Remmert, M and Biegert},
TITLE   = {{HHrep: {\it de novo} protein repeat detection and the origin of TIM barrels}},
YEAR    = {2006},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {34},
PAGES   = {W137-W142}
}

@ARTICLE{Soding:2006b,
AUTHOR  = {S\"oding, J. and Remmert, M and Biegert, A and Lupas, A. N.},
TITLE   = {{HHsenser: exhaustive transitive profile search detection using HMM-HMM  comparison}},
YEAR    = {2006},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {34},
PAGES   = {W374-W378}
}

@ARTICLE{Gruber:2006,
AUTHOR  = {Gruber, M. and S\"oding, J. and Lupas, A. N.},
TITLE   = {{Comparative analysis of coiled-coil prediction methods}},
YEAR    = {2006},
JOURNAL = {J. Struct. Biol.},
VOLUME  = {155},
PAGES   = {140-145}
}

@ARTICLE{Biegert:2006,
AUTHOR  = {Biegert, A and Remmert, M and S\"oding, J. and Lupas, A. N.},
TITLE   = {{The MPI Bioinformatics Toolkit for protein sequence analysis}},
YEAR    = {2006},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {34},
PAGES   = {W335-W339}
}

@ARTICLE{Albrecht:2006,
AUTHOR  = {Albrecht, R. and Zeth, K. and S\"oding, J. and Lupas, A. N. and Linke, D.},
TITLE   = {{Expression, crystallization and preliminary X-ray crystallographic studies of the outer membrane protein OmpW from Escherichia coli}},
YEAR    = {2006},
JOURNAL = {Acta. Crystallograph. Sect. F. Struct. Biol. Cryst. Commun.},
VOLUME  = {62},
PAGES   = {415-418}
}

@ARTICLE{Soding:2005b,
AUTHOR  = {S\"oding, J. and Biegert, A. and Lupas, A. N.},
TITLE   = {The {HHpred} interactive server for protein homology detection and structure prediction},
YEAR    = {2005},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {33},
PAGES   = {W244-W248}
}

@ARTICLE{Gruber:2005,
AUTHOR  = {Gruber, M. and S\"oding, J. and Lupas, A. N.},
TITLE   = {{REPPER--repeats and their periodicities in fibrous proteins}},
YEAR    = {2005},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {33},
PAGES   = {W239-W243}
}

@ARTICLE{Coles:2005,
AUTHOR  = {Coles, M. and Djuranovic, S. and S\"oding, J. and Frickey, T. and Koretke, K. and Truffault, V. and Martin, J. and Lupas, A. N.},
TITLE   = {{AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels}},
YEAR    = {2005},
JOURNAL = {Structure},
VOLUME  = {13},
PAGES   = {919-928}
}

@ARTICLE{Soding:2005a,
AUTHOR  = {S\"oding, J.},
TITLE   = {Protein homology detection by {HMM-HMM} comparison},
YEAR    = {2005},
JOURNAL = {Bioinformatics},
VOLUME  = {21},
PAGES   = {951-960}
}

@ARTICLE{Moussian:2005,
AUTHOR  = {Moussian, B. and S\"oding, J. and Schwarz, H. and N\"usslein-Volhard, C.},
TITLE   = {{Retroactive, a membrane-anchored extracellular protein related to vertebrate snake neurotoxin-like proteins, is required for cuticle organization in the larva of Drosophila melanogaster}},
YEAR    = {2005},
JOURNAL = {Dev. Dyn.},
VOLUME  = {233},
PAGES   = {1056-1063}
}

@ARTICLE{Djuranovic:2006,
AUTHOR  = {Djuranovic, S. and Rockel, B. and Lupas, A. N. and Martin, J.},
TITLE   = {{Characterization of AMA, a new AAA protein from Archaeoglobus and methanogenic archaea}},
YEAR    = {2006},
JOURNAL = {J. Struc. Biol.},
VOLUME  = {156},
PAGES   = {130-138}
}

@ARTICLE{Diemand:2006,
AUTHOR  = {Diemand, A. and Lupas, A. N.},
TITLE   = {{Modeling AAA+ ring complexes from monomeric structures}},
YEAR    = {2006},
JOURNAL = {J. Struc. Biol.},
VOLUME  = {156},
PAGES   = {230-243}
}

@ARTICLE{Ammelburg:2006,
AUTHOR  = {Ammelburg, M. and Frickey, T. and Lupas, A. N.},
TITLE   = {{Classification of AAA+ proteins}},
YEAR    = {2006},
JOURNAL = {J. Struc. Biol.},
VOLUME  = {156},
PAGES   = {2-11}
}

@ARTICLE{Becker:2006,
AUTHOR  = {Becker, E. and Meyer, V. and Madaoui, H. and Guerois, R.},
TITLE   = {{Detection of a tandem BRCT in Nbs1 and Xrs2 with functional implications in the DNA damage response}},
YEAR    = {2006},
JOURNAL = {Bioinformatics},
VOLUME  = {22},
PAGES   = {1289-1292}
}

@ARTICLE{Jin:2005,
AUTHOR  = {Jin, J. and Cai, Y. and Yao, T. and Gottschalk, A. J. and Florens, L. and Swanson, S. K. and Gutierrez, J. L. and Coleman, M. K. and Workman, J. L. and Mushegian, A. and Washburn, M. P. and Conaway, R. C. and Conaway, J. W.},
TITLE   = {{A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex}},
YEAR    = {2005},
JOURNAL = {J. Biol. Chem.},
VOLUME  = {280},
PAGES   = {41207-41212}
}

@ARTICLE{Chatterjee:2005,
AUTHOR  = {Chatterjee, I. and Richmond, A. and Putiri, E. and Shakes, D. C. and Singson, A.},
TITLE   = {{The Caenorhabditis elegans spe-38 gene encodes a novel four-pass integral membrane protein required for sperm function at fertilization}},
YEAR    = {2005},
JOURNAL = {Development},
VOLUME  = {132},
PAGES   = {2795-2808}
}

@ARTICLE{Dokudovskaya:2006,
AUTHOR  = {Dokudovskaya, S. and Williams, R. and Devos, D. and Sali, A. and Chait, B. T. and Rout, M. P.},
TITLE   = {{Protease accessibility laddering: a proteomic tool for probing protein structure}},
YEAR    = {2006},
JOURNAL = {Structure},
VOLUME  = {14},
PAGES   = {653-660}
}

@ARTICLE{Liu:2006,
AUTHOR  = {Liu, J. and Glazko, G. and Mushegian, A.},
TITLE   = {{Protein repertoire of double-stranded DNA bacteriophages}},
YEAR    = {2006},
JOURNAL = {Virus Res.},
VOLUME  = {117},
PAGES   = {68-80}
}

@ARTICLE{Tkaczuk:2006,
AUTHOR  = {Tkaczuk, K. L. and Obarska, A. and Bujnicki, J. M.},
TITLE   = {{Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis}},
YEAR    = {2006},
JOURNAL = {BMC Evo. Biol.},
VOLUME  = {6},
PAGES   = {6}
}

@ARTICLE{Devos:2006,
AUTHOR  = {Devos, D. and Dokudovskaya, S. and Williams, R. and Alber, F. and Eswar, N. and Chait, B. T. and Rout, M. P. and Sali, A.},
TITLE   = {{Simple fold composition and modular architecture of the nuclear pore complex}},
YEAR    = {2006},
JOURNAL = {PNAS},
VOLUME  = {103},
PAGES   = {2172-2177}
}

@ARTICLE{Boekhorst:2006,
AUTHOR  = {Boekhorst, J. and Helmer, Q. and Kleerebezem, M. and Siezen, R. J.},
TITLE   = {{Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria}},
YEAR    = {2006},
JOURNAL = {Microbiology-SGM},
VOLUME  = {152},
PAGES   = {273-280}
}

@ARTICLE{Neugebauer:2005,
AUTHOR  = {Neugebauer, H. and Herrmann, C. and Kammer, W. and Schwarz, G. and Nordheim, A. and Braun, V.},
TITLE   = {{ExbBD-dependent transport of maltodextrins through the novel MalA protein across the outer membrane of Caulobacter crescentus}},
YEAR    = {2005},
JOURNAL = {J. Bact.},
VOLUME  = {187},
PAGES   = {8300-8311}
}

@ARTICLE{Minakhin:2005,
AUTHOR  = {Minakhin, L. and Semenova, E. and Liu, J. and Vasilov, A. and Severinova, E. and Gabisonia, T. and Inman, R. and Mushegian, A. and Severinov, K.},
TITLE   = {{Genome sequence and gene expression of Bacillus anthracis bacteriophage Fah}},
YEAR    = {2005},
JOURNAL = {J. Mol. Biol.},
VOLUME  = {354},
PAGES   = {1-15}
}

@ARTICLE{Suhre:2005,
AUTHOR  = {Suhre, K.},
TITLE   = {{Gene and genome duplication in Acanthamoeba polyphaga Mimivirus}},
YEAR    = {2005},
JOURNAL = {J. Virology},
VOLUME  = {79},
PAGES   = {14095-14101}
}

@ARTICLE{Tilburn:2005,
AUTHOR  = {Tilburn, J. and Sanchez-Ferrero, J. C. and Reoyo, E. and Arst, H. N. and Penalva, M. A.},
TITLE   = {{Mutational analysis of the pH signal transduction component PalC of Aspergillus nidulans supports distant similarity to BRO1 domain family members}},
YEAR    = {2005},
JOURNAL = {Genetics},
VOLUME  = {171},
PAGES   = {393-401}
}

@ARTICLE{Kosinski:2005,
AUTHOR  = {Kosinski, J. and Feder, M. and Bujnicki, J. M.},
TITLE   = {{The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function}},
YEAR    = {2005},
JOURNAL = {BMC Bioinformatics},
VOLUME  = {6},
PAGES   = {172}
}

@ARTICLE{Gibson:2005,
AUTHOR  = {Gibson, A. and Lewis, A. P. and Affleck, K. and Aitken, A. J. and Meldrum, E. and Thompson, N.},
TITLE   = {{hCLCA1 and mCLCA3 are secreted non-integral membrane proteins and therefore are not ion channels}},
YEAR    = {2005},
JOURNAL = {J. Biol. Chem.},
VOLUME  = {280},
PAGES   = {27205-27212}
}

@ARTICLE{Hsiao:2006,
AUTHOR  = {Hsiao, N. H. and S\"oding, J. and Linke, D. and Wohlleben, W. and Takano, E.},
TITLE   = {{ScbA from Streptomyces coelicolor A3(2) has homology to unsaturated fatty acid synthase and can synthesise $\gamma$-butyrolactones}},
YEAR    = {2006},
JOURNAL = {Microbiology},
VOLUME  = {153},
PAGES   = {1394-1404}
}

@ARTICLE{Alva:2006,
AUTHOR  = {Alva Kullanja, V. and Ammelburg, M. and S\"oding, J. and Lupas, A. N.},
TITLE   = {{The origin of the histone fold}},
YEAR    = {2006},
JOURNAL = {BMC Struct. Biol.},
VOLUME  = {7},
PAGES   = {17}
}

@ARTICLE{Cerasoli:2005,
AUTHOR  = {Cerasoli, E. and Sharpe, B. K. and Woolfson, D. N.},
TITLE   = {{ZiCo: a peptide designed to switch folded state upon binding zinc}},
YEAR    = {2005},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME  = {127},
PAGES   = {15008-15009}
}

@ARTICLE{Lichtarge:1996,
AUTHOR  = {Lichtarge, O. and Bourne, H. R. and Cohen, F. E.},
TITLE   = {{An evolutionary trace method defines binding surfaces common to protein families}},
YEAR    = {1996},
JOURNAL = {J. Mol. Biol.},
VOLUME  = {257},
PAGES   = {342-358}
}

@ARTICLE{Hein:1989,
AUTHOR  = {Hein, J.},
TITLE   = {{A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given}},
YEAR    = {1989},
JOURNAL = {Mol. Biol. Evol.},
VOLUME  = {6},
PAGES   = {649-668}
}

@ARTICLE{Ye:2005,
AUTHOR  = {Ye, Y. and Godzik, A.},
TITLE   = {{Multiple flexible structure alignment using partial order graphs}},
YEAR    = {2005},
JOURNAL = {Bioinformatics},
VOLUME  = {21},
PAGES   = {2362-2369}
}

@ARTICLE{Edgar:2004,
AUTHOR  = {Edgar, R. C.},
TITLE   = {{MUSCLE: a multiple sequence alignment method with reduced time and space complexity}},
YEAR    = {2004},
JOURNAL = {BMC. Bioinformatics.},
VOLUME  = {5},
PAGES   = {113}
}

@ARTICLE{Przybylski:2004,
AUTHOR  = {Przybylski, D. and Rost, B.},
TITLE   = {{Improving fold recognition without folds}},
YEAR    = {2004},
JOURNAL = {J. Mol. Biol.},
VOLUME  = {341},
PAGES   = {255-269}
}

@ARTICLE{Zhu:2005,
AUTHOR  = {Zhu, J. and Weng, Z.},
TITLE   = {{FAST: a novel protein structure alignment algorithm}},
YEAR    = {2005},
JOURNAL = {Proteins},
VOLUME  = {58},
PAGES   = {618-627}
}

@ARTICLE{Zhang:2005b,
AUTHOR  = {Zhang, Y. and Skolnick, J.},
TITLE   = {{TM-align: a protein structure alignment algorithm based on the TM-score}},
YEAR    = {2005},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {33},
PAGES   = {2302-2309}
}

@ARTICLE{John:2003,
AUTHOR  = {John, B. and Sali, A.},
TITLE   = {{Comparative protein structure modeling by iterative alignment, model building and model assessment}},
YEAR    = {2003},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {31},
PAGES   = {3982-3992}
}

@ARTICLE{Zhang:2005a,
AUTHOR  = {Zhang, Y. and Arakaki, A. K. and Skolnick, J.},
TITLE   = {{TASSER: an automated method for the prediction of protein tertiary structures in CASP6}},
YEAR    = {2005},
JOURNAL = {Proteins},
VOLUME  = {61},
PAGES   = {91-98}
}

@ARTICLE{Rieping:2005,
AUTHOR  = {Rieping, W. and Habeck, M. and Nilges, M.},
TITLE   = {{Inferential structure determination}},
YEAR    = {2005},
JOURNAL = {Science},
VOLUME  = {309},
PAGES   = {303-306}
}

@ARTICLE{Pearson:1988,
AUTHOR  = {Pearson, W. R. and Lipman, D. J.},
TITLE   = {{Improved tools for biological sequence comparison}},
YEAR    = {1988},
JOURNAL = {Proc. Natl. Acad. Sci. U. S. A.},
VOLUME  = {85},
PAGES   = {2444-2448}
}

@ARTICLE{Mi:2005,
AUTHOR  = {Mi, H. and Lazareva-Ulitsky, B. and Loo, R. and Kejariwal, A. and Vandergriff, J. and Rabkin, S. and Guo, N. and Muruganujan, A. and Doremieux, O. and Campbell, M. J. and Kitano, H. and Thomas, P. D.},
TITLE   = {{The PANTHER database of protein families, subfamilies, functions and pathways}},
YEAR    = {2005},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {33},
PAGES   = {D284-D288}
}

@ARTICLE{Haft:2003,
AUTHOR  = {Haft, D. H. and Selengut, J. D. and White, O.},
TITLE   = {{The TIGRFAMs database of protein families}},
YEAR    = {2003},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {31},
PAGES   = {371-373}
}

@ARTICLE{Wu:2004,
AUTHOR  = {Wu, C. H. and Nikolskaya, A. and Huang, H. {\it et al.}},
TITLE   = {{PIRSF: family classification system at the Protein Information Resource}},
YEAR    = {2004},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {32},
PAGES   = {D112-D114}
}

@ARTICLE{Pearl:2005,
AUTHOR  = {Pearl, F. and Todd, A. and Sillitoe, I. {\it et al.}},
TITLE   = {{The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis}},
YEAR    = {2005},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {33},
PAGES   = {D247-D251}
}

@ARTICLE{Sonnhammer:1995,
AUTHOR  = {Sonnhammer, E. L. and Durbin, R.},
TITLE   = {A dot-matrix program with dynamic threshold control suited for genomic {DNA} and protein sequence analysis},
YEAR    = {1995},
JOURNAL = {Gene},
VOLUME  = {167},
PAGES   = {GC1-10}
}

@ARTICLE{Nagano:2002,
AUTHOR  = {Nagano, N. and Orengo, C. A. and Thornton, J. M.},
TITLE   = {One fold with many functions: the evolutionary relationships between {TIM} barrel families based on their sequences, structures and functions},
YEAR    = {2002},
JOURNAL = {J. Mol. Biol.},
VOLUME  = {321},
PAGES   = {741-765}
}

@ARTICLE{Branden:1991,
AUTHOR  = {Br\"and\'{e}n, C. I.},
TITLE   = {The {TIM} barrel -- the most frequently occurring folding motif in proteins },
YEAR    = {1991},
JOURNAL = {Curr. Opin. Struct. Biol.},
VOLUME  = {1},
PAGES   = {978-983}
}
 
@ARTICLE{Reardon:1995,
AUTHOR  = {Reardon, D. and Farber, G. K.},
TITLE   = {The structure and evolution of $\alpha/\beta$ barrel proteins},
YEAR    = {1995},
JOURNAL = {FASEB. J.},
VOLUME  = {9},
PAGES   = {497-503}
}

@ARTICLE{Copley:2000,
AUTHOR  = {Copley, R. R. and Bork, P.},
TITLE   = {Homology among $(\beta/\alpha)_8$ barrels: implications for the evolution of metabolic pathways},
YEAR    = {2000},
JOURNAL = {J. Mol. Biol.},
VOLUME  = {303},
PAGES   = {627-641}
}

@ARTICLE{Lang:2000,
AUTHOR  = {Lang, D. and Thoma, R. and Henn-Sax, M. and Sterner, R. and Wilmanns, M.},
TITLE   = {Structural evidence for evolution of the $\beta/\alpha$ barrel scaffold by gene duplication and fusion},
YEAR    = {2000},
JOURNAL = {Science},
VOLUME  = {289},
PAGES   = {1546-1550}
}

@ARTICLE{Forterre:1999,
AUTHOR  = {Forterre, P. and Philippe, H.},
TITLE   = {The last universal common ancestor (LUCA), simple or complex?
},
YEAR    = {1999},
JOURNAL = {Biol. Bull.},
VOLUME  = {196},
PAGES   = {373-375}
}

@ARTICLE{Wallner:2004,
AUTHOR  = {Wallner, B. and Fang, H. and Ohlson, T. and Frey-Skott, J. and Elofsson, A.},
TITLE   = {Using evolutionary information for the query and target improves fold recognition},
YEAR    = {2004},
JOURNAL = {Proteins},
VOLUME  = {54},
PAGES   = {342-350}
}

@ARTICLE{Gruber:2005,
AUTHOR  = {Gruber, M. and S\"oding, J. and Lupas, A. N.},
TITLE   = {{REPPER}--repeats and their periodicities in fibrous proteins},
YEAR    = {2005},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {33},
PAGES   = {W239-W243}
}

@ARTICLE{Coward:1998,
AUTHOR  = {Coward, E. and Drablos, F.},
TITLE   = {Detecting periodic patterns in biological sequences},
YEAR    = {1998},
JOURNAL = {Bioinformatics},
VOLUME  = {14},
PAGES   = {498-507}
}

@ARTICLE{McLachlan:1976,
AUTHOR  = {McLachlan, A. D. and Stewart, M.},
TITLE   = {The 14-fold periodicity in alpha-tropomyosin and the interaction with actin},
YEAR    = {1976},
JOURNAL = {J. Mol. Biol.},
VOLUME  = {103},
PAGES   = {271-298}
}
 
@ARTICLE{Salem:1999,
AUTHOR  = {Salem, G. M. and Hutchinson, E. G. and Orengo, C. A. and Thornton, J. M.},
TITLE   = {Correlation of observed fold frequency with the occurrence of local structural motifs},
YEAR    = {1999},
JOURNAL = {J. Mol. Biol.},
VOLUME  = {287},
PAGES   = {969-981}
}

@ARTICLE{Fani:1994,
AUTHOR  = {Fani, R. and Lio, P. and Chiarelli, I. and Bazzicalupo, M.},
TITLE   = {The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the {hisA} and {hisF} genes},
YEAR    = {1994},
JOURNAL = {J. Mol. Evol.},
VOLUME  = {38},
PAGES   = {489-495}
}

@ARTICLE{Zhang:2004,
AUTHOR  = {Zhang, Y. and Skolnick, J.},
TITLE   = {{Scoring function for automated assessment of protein structure template quality}},
YEAR    = {2004},
JOURNAL = {Proteins},
VOLUME  = {57},
PAGES   = {702-710}
}

@ARTICLE{Biegert:2009,
AUTHOR  = {Biegert, A. and S\"oding, J.},
TITLE   = {{Sequence context-specific profiles for homology searching}},
YEAR    = {2009},
JOURNAL = {Proc. Natl. Acad. Sci. U. S. A.},
VOLUME  = {106},
PAGES   = {3770-3775}
}

@ARTICLE{Biegert:2008,
AUTHOR  = {Biegert, A. and S\"oding, J.},
TITLE   = {{De novo identification of highly diverged protein repeats by probabilistic consistency}},
YEAR    = {2008},
JOURNAL = {Bioinformatics},
VOLUME  = {24},
PAGES   = {807-814}
}

@ARTICLE{Holmes:1998,
AUTHOR  = {Holmes, I. and Durbin, R.},
TITLE   = {{Dynamic programming alignment accuracy}},
YEAR    = {1998},
JOURNAL = {J. Comput. Biol.},
VOLUME  = {5},
PAGES   = {493-504}
}

@ARTICLE{Battey:2007,
AUTHOR  = {Battey, J. N. and Kopp, J. and Bordoli, L. and Read, R. J. and Clarke, N. D. and Schwede, T.},
TITLE   = {{Automated server predictions in CASP7}},
YEAR    = {2007},
JOURNAL = {Proteins},
VOLUME  = {69},
PAGES   = {68-82}
}

@ARTICLE{Wallner:2007,
AUTHOR  = {Wallner, B. and Larsson, P. and Elofsson, A.},
TITLE   = {{Pcons.net: protein structure prediction meta server}},
YEAR    = {2007},
JOURNAL = {Nucleic Acids Res.},
VOLUME  = {35},
PAGES   = {W369-W374}
}

@ARTICLE{Zhou:2009,
AUTHOR  = {Zhou, H. and Skolnick, J.},
TITLE   = {{Protein structure prediction by pro-Sp3-TASSER}},
YEAR    = {2009},
JOURNAL = {Biophys. J.},
VOLUME  = {96},
PAGES   = {2119-2127}
}

@ARTICLE{Kosinski:2005,
AUTHOR  = {Kosinski, J. and Gajda, M. J. and Cymerman, I. A. and Kurowski, M. A. and Pawlowski, M. and Boniecki, M. and Obarska, A. and Papaj, G. and Sroczynska-Obuchowicz, P. and Tkaczuk, K. L. and Sniezynska, P. and Sasin, J. M. and Augustyn, A. and Bujnicki, J. M. and Feder, M.},
TITLE   = {{FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6}},
YEAR    = {2005},
JOURNAL = {Proteins},
VOLUME  = {61},
PAGES   = {106-113}
}

@ARTICLE{Cozzetto:2005,
AUTHOR  = {Cozzetto, D. and Tramontano, A.},
TITLE   = {{Relationship between multiple sequence alignments and quality of protein comparative models}},
YEAR    = {2005},
JOURNAL = {Proteins},
VOLUME  = {58},
PAGES   = {151-157}
}

@ARTICLE{Jaroszewski:2002,
AUTHOR  = {Jaroszewski, L. and Li, W. and Godzik, A.},
TITLE   = {{In search for more accurate alignments in the twilight zone}},
YEAR    = {2002},
JOURNAL = {Protein. Sci.},
VOLUME  = {11},
PAGES   = {1702-1713}
}

@ARTICLE{Zhang:2008,
AUTHOR  = {Zhang, Y.},
TITLE   = {{I-TASSER server for protein 3D structure prediction}},
YEAR    = {2008},
JOURNAL = {BMC. Bioinformatics.},
VOLUME  = {9},
PAGES   = {40}
}

@ARTICLE{Xu:2008,
AUTHOR  = {Xu, J. and Jiao, F. and Yu, L.},
TITLE   = {{Protein structure prediction using threading}},
YEAR    = {2008},
JOURNAL = {Methods. Mol. Biol.},
VOLUME  = {413},
PAGES   = {91-121}
}

@ARTICLE{Chivian:2005,
AUTHOR  = {Chivian, D. and Kim, D. E. and Malmström, L. and Schonbrun, J. and Rohl, C. A. and Baker, D.},
TITLE   = {{Prediction of CASP6 structures using automated Robetta protocols}},
YEAR    = {2005},
JOURNAL = {Proteins},
VOLUME  = {61},
PAGES   = {157-166}
}

@ARTICLE{Zhou:2007,
AUTHOR  = {Zhou, H. and Pandit, S. B. and Lee, S. Y. and Borreguero, J. and Chen, H. and Wroblewska, L. and Skolnick, J.},
TITLE   = {{Analysis of TASSER-based CASP7 protein structure prediction results}},
YEAR    = {2007},
JOURNAL = {Proteins},
VOLUME  = {69},
PAGES   = {90-97}
}

@ARTICLE{Shackelford:2007,
AUTHOR  = {Shackelford, G. and Karplus, K.},
TITLE   = {{Contact prediction using mutual information and neural nets}},
YEAR    = {2007},
JOURNAL = {Proteins},
VOLUME  = {69},
PAGES   = {159-164}
}

@ARTICLE{Chothia:1986,
AUTHOR  = {Chothia, C. and Lesk, A. M.},
TITLE   = {{The relation between the divergence of sequence and structure in proteins}},
YEAR    = {1986},
JOURNAL = {EMBO J.},
VOLUME  = {5},
PAGES   = {823-826}
}