Theory and applications of the generalized born solvation model in macromolecular simulations Export

@article{Born2, abstract = {Generalized Born (GB) models provide an attractive way to include some thermodynamic aspects of aqueous solvation into simulations that do not explicitly model the solvent molecules. Here we discuss our recent experience with this model, presenting in detail the way it is implemented and parallelized in the AMBER molecular modeling code. We compare results using the GB model (or GB plus a surface-area based ldquohydrophobicrdquo term) to explicit solvent simulations for a 10 base-pair DNA oligomer, and for the 108-residue protein thioredoxin. A slight modification of our earlier suggested parameters makes the GB results more like those found in explicit solvent, primarily by slightly increasing the strength of NH\&bond;O and NH\&bond;N internal hydrogen bonds. Timing and energy stability results are reported, with an eye toward using these model for simulations of larger macromolecular systems and longer time scales. {\copyright} 2001 John Wiley \& Sons, Inc. Biopolymers (Nucleic Acid Sci) 56: 275-291, 2001}, address = {Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037}, author = {Tsui, Vickie and Case, David A.}, citeulike-article-id = {334431}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/1097-0282(2000)56:4%3C275::AID-BIP10024%3E3.0.CO;2-E}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/11754341}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=11754341}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/88511483/ABSTRACT}, day = {4}, doi = {10.1002/1097-0282(2000)56:4%3C275::AID-BIP10024%3E3.0.CO;2-E}, issn = {1097-0282}, journal = {Biopolymers}, keywords = {born, gb, simulation}, month = {December}, number = {4}, pages = {275--291}, posted-at = {2009-11-08 21:39:03}, priority = {2}, title = {Theory and applications of the generalized born solvation model in macromolecular simulations}, url = {http://dx.doi.org/10.1002/1097-0282(2000)56:4%3C275::AID-BIP10024%3E3.0.CO;2-E}, volume = {56}, year = {2000} }

TY - JOUR ID - Born2 L3 - citeulike-article-id:334431 N2 - Generalized Born (GB) models provide an attractive way to include some thermodynamic aspects of aqueous solvation into simulations that do not explicitly model the solvent molecules. Here we discuss our recent experience with this model, presenting in detail the way it is implemented and parallelized in the AMBER molecular modeling code. We compare results using the GB model (or GB plus a surface-area based ldquohydrophobicrdquo term) to explicit solvent simulations for a 10 base-pair DNA oligomer, and for the 108-residue protein thioredoxin. A slight modification of our earlier suggested parameters makes the GB results more like those found in explicit solvent, primarily by slightly increasing the strength of NH&bond;O and NH&bond;N internal hydrogen bonds. Timing and energy stability results are reported, with an eye toward using these model for simulations of larger macromolecular systems and longer time scales. © 2001 John Wiley & Sons, Inc. Biopolymers (Nucleic Acid Sci) 56: 275-291, 2001 IS - 4 JF - Biopolymers SN - 1097-0282 AD - Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 EP - 291 TI - Theory and applications of the generalized born solvation model in macromolecular simulations VL - 56 SP - 275 KW - born KW - gb KW - simulation AU - Tsui, Vickie AU - Case, David PY - 2000/12/04/ UR - http://dx.doi.org/10.1002/1097-0282(2000)56:4%3C275::AID-BIP10024%3E3.0.CO;2-E ER -