IAPBS: A programming interface to the adaptive Poisson-Boltzmann solver

Computational Science and Discovery

Volumn 5, Issue 1, 2012, Pages

  Konecny, Robert ^a   Baker, Nathan A ^a,b   McCammon, J Andrew ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION MODULE; ELECTROSTATIC CALCULATIONS; IMPLICIT SOLVENTS; INTERFACE LIBRARY; MOLECULAR DYNAMICS SIMULATIONS; POISSON-BOLTZMANN; PROGRAMMING INTERFACE;

HYPERSONIC AERODYNAMICS; MOLECULAR DYNAMICS;

ELECTROSTATICS;

EID: 84864397261     PISSN: 17494680     EISSN: 17494699     Source Type: Journal    
DOI: 10.1088/1749-4699/5/1/015005     Document Type: Article

References (30)

1. Ren P, Chun J, Thomas D G, Schnieders M J, Marucho M, Zhang J and Baker N A Biomolecular electrostatics and solvation: a computational perspective Q. Rev. Biophys. at press
2. Baker N A 2005 Improving implicit solvent simulations: a Poisson-centric view Curr. Opin. Struct. Biol. 15 137-43
3. Baker N A, Bashford D and Case D A 2006 Implicit solvent electrostatics in biomolecular simulation New Algorithms for Macromolecular Simulation (Lecture Notes in Computational Science and Engineering vol 49) ed B Leimkuhler, C Chipot, R Elber, A Laaksonen, A Mark, T Schlick, C Schütte and R Skeel (Berlin: Springer) pp 263-95
4. Roux B and Simonson T 1999 Implicit solvent models Biophys. Chem. 78 1-20 (Pubitemid 29206654)
5. Roux B 2001 Implicit solvent models Computational Biochemistry and Biophysics ed O M Becker, A D Mackerell, B Roux and M Watanabe (New York: Dekker) pp 133-52
6. Baker N A, Sept D, Joseph S, Holst M J and McCammon J A 2001 Electrostatics of nanosystems: application to microtubules and the ribosome Proc. Natl Acad. Sci. USA 98 10037-41 (Pubitemid 32802969)
7. Davis M E and McCammon J A 1990 Electrostatics in biomolecular structure and dynamics Chem. Rev. 90 509-21
8. Honig B and Nicholls A 1995 Classical electrostatics in biology and chemistry Science 268 1144-9
9. Trylska J, Konecny R, Tama F, Brooks C L and McCammon A J 2004 Ribosome motions modulate electrostatic properties Biopolymers 74 423-31 (Pubitemid 39128058)
10. Konecny R, Trylska J, Tama F, Zhang D, Baker N A, Brooks C L and McCammon J A 2006 Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids Biopolymers 82 106-20 (Pubitemid 43798159)
11. Holst M 2001 Adaptive numerical treatment of elliptic systems on manifolds Adv. Comput. Math. 15 139-91 (Pubitemid 33634300)
12. Bank R E and Holst M 2003 A new paradigm for parallel adaptive meshing algorithms SIAM Rev. 45 291
13. Holst M and Saied F 1993 Multigrid solution of the Poisson-Boltzmann equation J. Comput. Chem. 14 105-13
14. Holst M J and Saied F 1995 Numerical solution of the nonlinear Poisson-Boltzmann equation: developing more robust and efficient methods J. Comput. Chem. 16 337-64
15. Case D A et al 2012 AMBER 12 (San Francisco, CA: University of California)
16. Brooks B R et al 2009 CHARMM: the biomolecular simulation program J. Comput. Chem. 30 1545-615
17. Phillips J C, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R D, Kale L and Schulten K 2005 Scalable molecular dynamics with NAMD J. Comput. Chem. 26 1781-02 (Pubitemid 43078511)
18. Rick S W and Berne B J 1994 The aqueous solvation of water: a comparison of continuum methods with molecular dynamics J. Am. Chem. Soc. 116 3949-54 (Pubitemid 24980982)
19. Nina M, Beglov D and Roux B 1997 Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations J. Phys. Chem. B 101 5239-48 (Pubitemid 127609289)
20. Swanson J M J, Wagoner J A, Baker N A and McCammon J A 2007 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
21. Dolinsky T J, Nielsen J E, McCammon J A and Baker N A 2004 PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Nucleic Acids Res. 32 W665-7 (Web Server) (Pubitemid 38997419)
22. Unni S, Huang Y, Hanson R M, Tobias M, Krishnan S, Li W W, Nielsen J E and Baker N A 2011 Web servers and services for electrostatics calculations with APBS and PDB2PQR J. Comput. Chem. 32 1488-91
23. Baker N A 2004 Poisson-Boltzmann methods for biomolecular electrostatics Methods in Enzymology vol 383 ed L Brand and M L Johnson (New York: Academic) pp 94-118 (Pubitemid 38401788)
24. Dong F, Olsen B and Baker N A 2008 Computational Methods for Biomolecular Electrostatics Methods in Cell Biology vol 84 ed J J Correia and H W Detrich (New York: Academic) pp 843-70
25. Wagoner J A and Baker N A 2006 Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms Proc. Natl Acad. Sci. USA 103 8331-6 (Pubitemid 43838455)
26. Luo R, David L and Gilson M K 2002 Accelerated Poisson-Boltzmann calculations for static and dynamic systems J. Comput. Chem. 23 1244-53 (Pubitemid 35009216)
27. Izaguirre J A, Reich S and Skeel R D 1999 Longer time steps for molecular dynamics J. Chem. Phys. 110 9853-64
28. Kollman P A et al 2000 Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Acc. Chem. Res. 33 889-97 (Pubitemid 32056774)
29. McGee D, Miller B III and Swails J 2012 MMPBSA.py: a script for performing molecular mechanics Poisson Boltzmann surface area calculation to find free energies of binding
30. Schrödinger L L C 2012 The PyMOL molecular graphics system, version 1.4r1