iAPBS: a programming interface to the adaptive Poisson–Boltzmann solver
作者： Robert Konecny , Nathan A Baker , J Andrew McCammon
DOI: 10.1088/1749-4699/5/1/015005
关键词:
摘要: … adaptive Poisson–Boltzmann solver (APBS) is a state-of-the-art suite for performing Poisson–Boltzmann electrostatic … to the APBS library of electrostatic calculation routines. The …
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Nathan A. Baker, Donald Bashford, David A. Case, Implicit Solvent Electrostatics in Biomolecular Simulation Springer, Berlin, Heidelberg. pp. 263- 295 ,(2006) , 10.1007/3-540-31618-3_15
W. L. Delano, The PyMOL Molecular Graphics System DeLano Scientific. ,(2002)
John N Abelson, Melvin I Simon, Ludwig Brand, Michael L Johnson, Numerical computer methods Academic Press. ,(1992)
Nathan A. Baker, Poisson-Boltzmann methods for biomolecular electrostatics. Methods in Enzymology. ,vol. 383, pp. 94- 118 ,(2004) , 10.1016/S0076-6879(04)83005-2
Ray Luo, Laurent David, Michael K. Gilson, Accelerated Poisson-Boltzmann calculations for static and dynamic systems. Journal of Computational Chemistry. ,vol. 23, pp. 1244- 1253 ,(2002) , 10.1002/JCC.10120
Jessica M. J. Swanson, Jason A. Wagoner, Nathan A. Baker, J. A. McCammon, Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric Functions. Journal of Chemical Theory and Computation. ,vol. 3, pp. 170- 183 ,(2007) , 10.1021/CT600216K
Peter A. Kollman, Irina Massova, Carolina Reyes, Bernd Kuhn, Shuanghong Huo, Lillian Chong, Matthew Lee, Taisung Lee, Yong Duan, Wei Wang, Oreola Donini, Piotr Cieplak, Jaysharee Srinivasan, David A. Case, Thomas E. Cheatham, Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models Accounts of Chemical Research. ,vol. 33, pp. 889- 897 ,(2000) , 10.1021/AR000033J
J. A. Wagoner, N. A. Baker, Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms Proceedings of the National Academy of Sciences of the United States of America. ,vol. 103, pp. 8331- 8336 ,(2006) , 10.1073/PNAS.0600118103
Randolph E. Bank, Michael Holst, A New Paradigm for Parallel Adaptive Meshing Algorithms SIAM Review. ,vol. 45, pp. 291- 323 ,(2003) , 10.1137/S003614450342061
Robert Konecny, Joanna Trylska, Florence Tama, Deqiang Zhang, Nathan A. Baker, Charles L. Brooks, J. A. McCammon, Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers. ,vol. 82, pp. 106- 120 ,(2006) , 10.1002/BIP.20409