Software

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Further reading

Contents

  1. 1 Primary citations
    1. 1.1 APBS
    2. 1.2 PDB2PQR
  2. 2 Reviews
  3. 3 Methodology
    1. 3.1 Numerical solvers
    2. 3.2 Solvation models
    3. 3.3 pKa methods
    4. 3.4 Force fields
  4. 4 Software
  5. 5 Applications

Primary citations

Please use these references when citing any work performed with PDB2PQR or APBS.  A full list of publications from the Baker group can be found at http://mypubs.wordpress.com.

APBS

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA, 98, 10037-41, 2001.  http://dx.doi.org/10.1073/pnas.181342398

PDB2PQR

Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007.  http://dx.doi.org/10.1093/nar/gkm276

Reviews

  • Chen AA, Marucho M, Baker NA, Pappu RV. Simulations of RNA interactions with monovalent ions. Methods in Enzymology, 469, 411-432, 2009.  http://dx.doi.org/10.1016/S0076-6879(09)69020-0.  
  • Dong F, Olsen B, Baker NA. Computational Methods for Biomolecular Electrostatics. Methods in Cell Biology: Biophysical Tools for Biologists, 84, 843-870, 2008.  http://dx.doi.org/10.1016/S0091-679X%2807%2984026-X.  
  • Baker NA, Bashford D, Case DA. Implicit solvent electrostatics in biomolecular simulation. New Algorithms for Macromolecular Simulation. Leimkuhler B, Chipot C, Elber R, Laaksonen A, Mark A, Schlick T, Schutte C, Skeel R, eds., 2006.  http://dx.doi.org/10.1007/3-540-31618-3_15.
  • Baker NA. Improving implicit solvent simulations: a Poisson-centric view. Curr Opin Struct Biol, 15, 137-43, 2005.  http://dx.doi.org/10.1016/j.sbi.2005.02.001.
  • Baker NA. Biomolecular applications of Poisson-Boltzmann methods. Reviews in Computational Chemistry. Lipkowitz KB, Larter R, Cundari TR., 21, 2005.
  • Baker NA, McCammon JA. Electrostatic interactions. Structural Bioinformatics. Weissig H, Bourne PE, eds., 2005.
  • Baker NA. Poisson-Boltzmann methods for biomolecular electrostatics. Methods in Enzymology, 383, 94-118, 2004.  http://dx.doi.org/10.1016/S0076-6879%2804%2983005-2.

Methodology

Numerical solvers

  • Chen Z, Baker NA, Wei GW. Differential geometry based solvation model II: Lagrangian formulation. J Math Biol, accepted.  http://dx.doi.org/10.1007/s00285-011-0402-z  Describes a surface-based approach to equations associated with new coupled models of polar and non-polar solvation.
  • Chen Z, Baker NA, Wei GW. Differential geometry based solvation model I: Eulerian formulation, J Comput Phys, 229, 8231-58, 2010.  http://dx.doi.org/10.1016/j.jcp.2010.06.036.  Describes a volume-based approach to equations associated with new coupled models of polar and non-polar solvation.
  • Schnieders MJ, Baker NA, Ren P, Ponder JW. Polarizable Atomic Multipole Solutes in a Poisson-Boltzmann Continuum. J Chem Phys, 126, 124114, 2007.  http://dx.doi.org/10.1063/1.2714528.  
  • Baker NA, Sept D, Holst MJ, McCammon JA. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM J Res Devel, 45, 427-38, 2001.  http://dx.doi.org/10.1147/rd.453.0427.
  • Holst M, Baker NA, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: algorithms and examples. J Comput Chem, 21, 1319-42, 2000.  http://is.gd/7DRxJl.
  • Baker N, Holst M, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II: refinement schemes based on solvent accessible surfaces. J Comput Chem, 21, 1343-52, 2000.  http://is.gd/HhZo9J.
  • Stone JE, Gohara D, Shi G. OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems. Computing in Science & Engineering, 12 (3), 66-73.  http://dx.doi.org/10.1109/MCSE.2010.69.

Solvation models

  • Chen Z, Baker NA, Wei GW. Differential geometry based solvation model II: Lagrangian formulation. J Math Biol, accepted.  http://dx.doi.org/10.1007/s00285-011-0402-z  Describes a surface-based approach to equations associated with new coupled models of polar and non-polar solvation.
  • Chen Z, Baker NA, Wei GW. Differential geometry based solvation model I: Eulerian formulation, J Comput Phys, 229, 8231-58, 2010.  http://dx.doi.org/10.1016/j.jcp.2010.06.036.  Describes a volume-based approach to equations associated with new coupled models of polar and non-polar solvation.
  • Dong F, Wagoner JA, Baker NA. Assessing the performance of implicit solvation models at a nucleic acid surface. Phys Chem Chem Phys, 10, 4889-902, 2008.  http://dx.doi.org/10.1039/b807384h.
  • Cerutti DS, Baker NA, McCammon JA. Solvent Reaction Field Potential inside an Uncharged Globular Protein: A Bridge between Implicit and Explicit Solvent Models? J Chem Phys,127, 155101, 2007.  http://dx.doi.org/10.1063/1.2771171.
  • Swanson JMJ, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: lessons learned with atom-centered dielectric functions. J Chem Theory Comput, 3, 170-83, 2007.  http://dx.doi.org/10.1021/ct600216k.
  • Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA, 103, 8331-6, 2006.  http://dx.doi.org/10.1073/pnas.0600118103.
  • Wagoner J, Baker NA. Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models. J Comput Chem, 25, 1623-9, 2004.  http://dx.doi.org/10.1002/jcc.20089.

pKa methods

  • Li H, Robertson AD, Jensen JH. Very fast empirical prediction and rationalization of protein pKa values. Proteins 61 (4) 704-21, 2005.  http://dx.doi.org/10.1002/prot.20660.  Original PROPKA paper used by PDB2PQR.
  • Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32, W665-7, 2004.  http://dx.doi.org/10.1093/nar/gkh381.  Original PDB2PQR paper.
  • Czodrowski P, Dramburg I, Sotriffer CA, Klebe G. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes. Proteins 65 (2) 424-37, 2006.  http://dx.doi.org/10.1002/prot.21110.  Description of PEOE method used for ligand parameterization in PDB2PQR.  

Force fields

  • Wang J, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21 (12) 1049-74, 2000.  http://www3.interscience.wiley.com/cgi-bin/abstract/72511509/ABSTRACT.  Paper describing the "AMBER" force field used by PDB2PQR.
  • Tan C, Yang L, Luo R. How Well Does Poisson-Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis. J Phys Chem B 110 (37) 18680-7, 2006. http://dx.doi.org/10.1021/jp063479b.   Paper describing the "TYL06" force field used by PDB2PQR.
  • Sitkoff D, Sharp KA, Honig B. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J Phys Chem 98 (7) 1978-88, 1994.  http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1994/98/i07/pdf/j100058a043.pdf.  Paper described the "PARSE" force field used by PDB2PQR.
  • Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity -- rapid access to atomic charges. Tetrahedron 36 (22) 3219-28, 1980. http://dx.doi.org/10.1016/0040-4020(80)80168-2.  Description of original charge assignment method used in PDB2PQR.
  • MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczer a, Yin D, Karplus M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J Phys Chem B 102 (18) 3586-616, 1998. http://dx.doi.org/10.1021/jp973084f.  Paper describing the "CHARMM" force field used by PDB2PQR.
  • Czodrowski P, Dramburg I, Sotriffer CA, Klebe G. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes. Proteins 65 (2) 424-37, 2006.  http://dx.doi.org/10.1002/prot.21110.  Description of PEOE method used for ligand parameterization in PDB2PQR.  
  • Swanson JMJ, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: lessons learned with atom-centered dielectric functions. J Chem Theory Comput, 3, 170-83, 2007.  http://dx.doi.org/10.1021/ct600216k.

Software

  • Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32, W665-7, 2004.  http://dx.doi.org/10.1093/nar/gkh381.  Original PDB2PQR paper.
  • Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA, 98, 10037-41, 2001.  http://dx.doi.org/10.1073/pnas.181342398.  Original APBS paper.
  • Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007.  http://dx.doi.org/10.1093/nar/gkm276.  Updated PDB2PQR paper.
  • Unni S, Huang Y, Hanson RM, Tobias M, Krishnan S, Li WW, Nielsen JE, Baker NA. Web servers and services for electrostatics calculations with APBS and PDB2PQR. J Comput Chem, 32 (7), 1488-1491, 2011.  http://dx.doi.org/10.1002/jcc.21720.  Development of web services for APBS and PDB2PQR.
  • Callenberg KM, Choudhary OP, de Forest GL, Gohara DW, Baker NA, Grabe M. APBSmem: A graphical interface for electrostatic calculations at the membrane. PLoS ONE, 5, e12722, 2010.  http://dx.doi.org/10.1371/journal.pone.0012722.  Software for setting up APBS calculations for membrane protein calculations.
  • Vitalis A, Baker NA, McCammon JA. ISIM: a program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules. Mol Sim, 30, 45-61, 2004.  http://dx.doi.org/10.1080/08927020310001597862.
  • Baker NA, Sept D, Holst MJ, McCammon JA. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM J Res Devel, 45, 427-38, 2001.  http://dx.doi.org/10.1147/rd.453.0427.

Applications

This list is very incomplete.  Please feel free to suggest additional papers to include.
  1. Silva JR, Pan H, Wu D, Nekouzadeh A, Decker KF, Cui J, Baker NA, Sept D, Rudy Y. A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential. Proc Natl Acad Sci USA, 106, 11102-6, 2009.  http://dx.doi.org/10.1073/pnas.0904505106.  
  2. Zhang X, Bajaj CL, Kwon B, Dolinsky TJ, Nielsen JE, Baker NA. Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity.  Multiscale Model Simul, 5, 1196-213, 2006.  http://dx.doi.org/10.1137/050647670.
  3. Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL III, McCammon JA. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers,82, 106-20, 2006.  http://dx.doi.org/10.1002/bip.20409.  
  4. Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J, 88, 1659-1666, 2005.  http://dx.doi.org/10.1529/biophysj.104.053850.
  5. Zhang D, Konecny R, Baker NA, McCammon JA. Electrostatic interaction between RNA and protein capsid in CCMV simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers, 75, 325-337, 2004.  http://dx.doi.org/10.1002/bip.20120.
  6. Sept D, Baker NA, McCammon JA. The physical basis of microtubule stability. Protein Sci, 12, 2257-61, 2003.  http://dx.doi.org/10.1110/ps.03187503.
  7. Lin JH, Baker NA, McCammon JA. Bridging implicit and explicit solvent approaches for membrane electrostatics. Biophys J, 83, 1374-9, 2002.  http://dx.doi.org/10.1016/S0006-3495%2802%2973908-8.
  8. Ma C, Baker NA, Joseph S, McCammon JA. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. J Am Chem Soc, 124, 1438-42, 2002.  http://dx.doi.org/10.1021/ja016830+.