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<chapter id="introduction-sect"> <title>Introduction</title>

	<para>APBS is a software package for the numerical solution of the
		Poisson-Boltzmann equation (PBE), one of the most popular continuum models
		for describing electrostatic interactions between molecular solutes in
		salty, aqueous media. Continuum electrostatics plays an important role in
		several areas of biomolecular simulation, including:
		<itemizedlist>
			<listitem>
				<para>simulation of diffusional processes to determine ligand-protein
					and protein-protein binding kinetics,</para>
			</listitem>
			<listitem>
				<para>implicit solvent molecular dynamics of biomolecules,</para>
			</listitem>
			<listitem>
				<para>solvation and binding energy calculations to determine
					ligand-protein and protein-protein equilibrium binding constants and
					aid in rational drug design,</para>
			</listitem>
			<listitem>
				<para>and biomolecular titration studies.</para>
			</listitem>
		</itemizedlist>
		APBS was designed to efficiently evaluate electrostatic properties for
		such simulations for a wide range of length scales to enable the investigation
		of molecules with tens to millions of atoms.</para>

	<para>APBS uses <ulink url="http://www.fetk.org/">PMG</ulink> to solve the
		Poisson-Boltzmann equation numerically.  PMG is developed and maintained
		by the <ulink url="http://www.scicomp.ucsd.edu/~mholst/">Holst Research
			Group</ulink> at UC San Diego, and is designed to solve the nonlinear
		Poisson-Boltzmann equation and similar problems with linear space and time
		complexity through the use of box methods, inexact Newton methods, and
		algebraic multilevel methods.  More information about PMG may be found at
		<ulink url="http://www.fetk.org">http://www.fetk.org</ulink>.
	</para>

	<para>Additionally, APBS uses the "Aqua" library, a version of Holst group <ulink url="http://www.fetk.org/">PMG</ulink> that has been specially optimized by <ulink url="http://koehllab.genomecenter.ucdavis.edu/">Patrice Koehl</ulink> for improved memory usage and speed when solving the Poisson-Boltzmann equation.</para>

	<para>APBS also uses <ulink url="http://www.fetk.org/">FEtk</ulink>  to
		solve the Poisson-Boltzmann equation numerically.  FEtk is developed and
		maintained by the <ulink url="http://www.scicomp.ucsd.edu/~mholst/">Holst
			Research Group</ulink> at UC San Diego, and is designed to solve general
		coupled systems of nonlinear partial differential equations accurately and
		efficiently using adaptive multilevel finite element methods, inexact
		Newton methods, algebraic multilevel methods.   More information about
		FEtk may be found at 
		<ulink url="http://www.fetk.org">http://www.fetk.org</ulink>.
	</para>

	<formalpara> <title>Financial support</title>
		<para>The development of APBS has been supported financially by:
			<itemizedlist>
				<listitem>
					<para><ulink url="http://www.nih.gov">National Institutes of 
							Health</ulink> (grant GM069702-01)</para>
				</listitem>
				<listitem>
					<para><ulink url="http://www.npaci.edu">National Partnership for Advanced
							Computational Infrastructure</ulink></para>
				</listitem>
				<listitem>
					<para><ulink url="http://nbcr.sdsc.edu">National Biomedical Computation
							Resource</ulink></para>
				</listitem>
			</itemizedlist>
		</para>
	</formalpara>

	<formalpara id="citing"> <title>Citing APBS</title>
		<para>
			Please acknowledge your use of APBS by citing:
			<blockquote> 
				<para> 
					<ulink url="http://www.pnas.org/cgi/content/abstract/98/18/10037"> 
						Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA.  Electrostatics
						of nanosystems: application to microtubules and the ribosome.
						<citetitle>Proc Natl Acad Sci USA</citetitle> 98, 10037-10041, 2001.
					</ulink>  
				</para> 
			</blockquote>
		</para>
	</formalpara>
	<formalpara id="citing2"> <title>Citing FEtk and PMG</title>
		<para>
			Please acknowledge your use of PMG and FEtk by citing:
			<blockquote> 
				<para> 
					M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann
					equation.  <citetitle>J. Comput. Chem.</citetitle>, 14 (1993), pp.
					105-113.
				</para>
				<para>
					M. Holst and F. Saied, Numerical solution of the nonlinear
					Poisson-Boltzmann equation: Developing more robust and efficient
					methods.  <citetitle>J. Comput. Chem.</citetitle>, 16 (1995), pp.
					337-364.
				</para>
				<para>
					M. Holst, Adaptive numerical treatment of elliptic systems on
					manifolds. <citetitle>Advances in Computational
						Mathematics</citetitle>, 15 (2001), pp. 139-191.
				</para>
				<para>
					R. Bank and M. Holst, A New Paradigm for Parallel Adaptive Meshing
					Algorithms. <citetitle>SIAM Review</citetitle>, 45 (2003), pp.
					291-323.
				</para>
			</blockquote>
		</para>

	</formalpara>

	<formalpara id="authors"> <title>Contributing authors</title>
		<para>APBS was primarily written by Nathan Baker during his graduate work
			with J. Andrew McCammon and Michael Holst and extensively developed over
			the subsequent years.  APBS uses several libraries written by Mike Holst
			and members of the Holst group, including:  
			<ulink url="http://scicomp.ucsd.edu/~mholst/codes/pmg/index.html">PMG</ulink> 
			(multigrid solver for Cartesian mesh discretization), 
			<ulink url="http://www.fetk.org">FEtk</ulink> 
			(provides finite element framework, error estimators, and solvers), and 
			<ulink url="http://scicomp.ucsd.edu/~mholst/codes/maloc/index.html">MALOC
			</ulink> (hardware abstraction library for code portability).
			Additionally, a number of people have made important contributions to enhance
			APBS functionality and usability.  The full author list (in alphabetical
			order) is:
			<itemizedlist>
				<listitem>
					<para>Nathan A. Baker</para>
					<para>Primary author</para> 
				</listitem>
				<listitem>
					<para>Steve Bond</para>
					<para>Contributor:  FEtk library compatibility and Vopot functions</para>
				</listitem>
				<listitem>
					<para>Larry Canino</para>
					<para>Contributor: solvent accessibility function modification</para>
				</listitem>
				<listitem>
					<para>Todd Dolinsky</para>
					<para>Developer and contributor: Python
						wrappers, PDB2PQR, output
						logging, examples, and other
						tools</para> 
				</listitem>
				<listitem> 
					<para>Adrian Elcock</para>
					<para>Contributor: parameter files</para>
				</listitem>
				<listitem>
					<para>David Gohara</para>
					<para>Developer</para>
				</listitem>
				<listitem>
					<para>Michael J. Holst</para>
					<para>Advisor and author of several routines scattered about APBS,
						and author of PMG (the multigrid library used by this code), author
						of MALOC (hardware abstraction library used by this code), author
						of FEtk (finite element library incorporated in developmental
						versions of this code)
					</para>
				</listitem>
				<listitem>
					<para>Adrian Kaats</para>
					<para>Contributor:  multivalue.c</para>
				</listitem>
				<listitem>
					<para>Robert Konecny</para>
					<para>Contributor: parameters, CHARMM FORTRAN interface</para>
				</listitem>
				<listitem>
					<para>Jung-Hsin Lin</para>
					<para>Contributor:  OpenDX to MOLMOL conversion</para>
				</listitem>
				<listitem>
					<para>Chiansan Ma</para>
					<para>Contributor: format conversion scripts</para>
				</listitem>
				<listitem>
					<para>J. Andrew McCammon</para>
					<para>Advisor, financial and equipment support, functionality
						suggestions</para> 
				</listitem> 
				<listitem>
					<para>Jens Nielsen</para>
					<para>Contributor: PDB2PQR</para>
				</listitem>
				<listitem>
					<para>Jay Ponder</para>
					<para>Contributor:  TINKER Interface</para>
				</listitem>
				<listitem>
					<para>Michael Schnieders</para>
					<para>Contributor:  Polarizable atomic multipole routines, TINKER 
						interface</para>
				</listitem>
				<listitem>
					<para>David Sept</para>
					<para> Contributor:  scripts and tools, VMD compatibility, general
						suggestions about functionality </para>
				</listitem>
				<listitem>
					<para>Tongye Shen</para>
					<para>Contributor:  finite element mesh generation</para>
				</listitem>
				<listitem>
					<para>Justin Xiang</para>
					<para>Contributor:  generalized Born
						Python utilities</para>
				</listitem>
			</itemizedlist>
		</para>
	</formalpara>
</chapter>