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@article{MBB_2010_5_a6, author = {A. V. Finkelstein and L. B. Pereyaslavets}, title = {New polarizable atomic force fields for calculation of non-bonded interactions in explicit and implicit aqueous surrounding}, journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika}, pages = {138--149}, publisher = {mathdoc}, volume = {5}, year = {2010}, language = {ru}, url = {http://geodesic.mathdoc.fr/item/MBB_2010_5_a6/} }
TY - JOUR AU - A. V. Finkelstein AU - L. B. Pereyaslavets TI - New polarizable atomic force fields for calculation of non-bonded interactions in explicit and implicit aqueous surrounding JO - Matematičeskaâ biologiâ i bioinformatika PY - 2010 SP - 138 EP - 149 VL - 5 PB - mathdoc UR - http://geodesic.mathdoc.fr/item/MBB_2010_5_a6/ LA - ru ID - MBB_2010_5_a6 ER -
%0 Journal Article %A A. V. Finkelstein %A L. B. Pereyaslavets %T New polarizable atomic force fields for calculation of non-bonded interactions in explicit and implicit aqueous surrounding %J Matematičeskaâ biologiâ i bioinformatika %D 2010 %P 138-149 %V 5 %I mathdoc %U http://geodesic.mathdoc.fr/item/MBB_2010_5_a6/ %G ru %F MBB_2010_5_a6
A. V. Finkelstein; L. B. Pereyaslavets. New polarizable atomic force fields for calculation of non-bonded interactions in explicit and implicit aqueous surrounding. Matematičeskaâ biologiâ i bioinformatika, Tome 5 (2010), pp. 138-149. http://geodesic.mathdoc.fr/item/MBB_2010_5_a6/
[1] Shaw D. E., Maragakis P., Lindorff-Larsen K., Piana S., Dror R. O., Eastwood M. P., Bank J. A., Jumper J. M., Salmon J. K., Shah Y., Wriggers W., “Atom-level characterization of structural dynamics of proteins”, Science, 330 (2010), 341–346 <ext-link ext-link-type='doi' href='https://doi.org/10.1126/science.1187409'>10.1126/science.1187409</ext-link>
[2] Lindorff-Larsen K., Piana S., Palmo K., Maragakis P., Klepeis J. L., Dror R. O., Shaw D. E., “Improved side-chain torsion potentials for the Amber ff99SB protein force field”, Proteins, 78 (2010), 1950–1958
[3] Warshel A., Lifson S., “Consistent force field calculations. II. Crystal structures, sublimation energies, molecular and lattice vibrations, molecular conformations, and enthalpies of alkanes”, J. Chem. Phys., 53 (1970), 582–594 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1674031'>10.1063/1.1674031</ext-link>
[4] Hagler A. T., Huler E., Lifson S., “Energy functions for peptides and proteins. I. Derivation of a consistent force fields including the hydrogen bond from amide crystals”, J. Am. Chem. Soc., 96 (1974), 5319–5327 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja00824a004'>10.1021/ja00824a004</ext-link>
[5] Hagler A. T., Lifson S., “Energy functions for peptides and proteins. II. The amide hydrogen bond and calculation of amide crystal properties”, J. Am. Chem. Soc., 96 (1974), 5327–5335 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja00824a005'>10.1021/ja00824a005</ext-link>
[6] Levitt M., Hirshberg M., Sharon R., Daggett V., “Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution”, Comput. Phys. Commun., 91 (1995), 215–231 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0010-4655(95)00049-L'>10.1016/0010-4655(95)00049-L</ext-link>
[7] MacKerell A. D., Jr., Bashford D., Bellott M., Dunbrack R. L., Jr., Evanseck J. D., Field M. J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F. T. K., Mattos C., Michnick S., Ngo T., Nguyen D. T., Prodhom B., Reiher W. E., III, Roux B., Schlenkrich M., Smith J. C., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., Karplus M., “All-atom empirical potential for molecular modeling and dynamics studies of proteins”, J. Phys. Chem. B, 102 (1998), 3586–3616 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/jp973084f'>10.1021/jp973084f</ext-link>
[8] Jorgensen W. L., Maxwell D. S., Tirado-Rives J., “Development and testing of the opls allatom force field on conformational energetics and properties of organic liquids”, J. Am. Chem. Soc., 118 (1996), 11225–11236 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja9621760'>10.1021/ja9621760</ext-link>
[9] Halgren T. A., “Merck Molecular Force Field. I. Basis, form, parameterization and performance of MMFF94”, J. Comput. Chem., 17 (1995), 490–519 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P'>10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P</ext-link>
[10] Wang J., Wolf R. M., Caldwell J. W., Kollman P. A., Case D. A., “Development and testing of a general Amber force fields”, J. Comput. Chem., 25 (2004), 1157–1174 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/jcc.20035'>10.1002/jcc.20035</ext-link>
[11] Kollman P. A., “Free energy calculations: Applications to chemical and biochemical phenomena”, Chem. Rev., 93 (1993), 2395–2417 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/cr00023a004'>10.1021/cr00023a004</ext-link>
[12] Onufriev A., Bashford D., Case D., “Exploring protein native states and large-scale conformational changes with a modified generalized born model”, Proteins, 55 (2004), 383–394 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/prot.20033'>10.1002/prot.20033</ext-link>
[13] Khoruzhii O. V., Donchev A. G., Galkin N. G., Illarionov A. A., Olevanov M. A., Ozrin V. D., Queen C., Tarasov V. I., “Application of a polarizable force field to calculations of relative protein-ligand binding affinities”, Proc. Natl. Acad. Sci. USA, 105 (2008), 10378–10383 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.0803847105'>10.1073/pnas.0803847105</ext-link>
[14] Roux B., Simonson T., “Implicit solvent models”, Biophys. Chem., 78 (1999), 1–20 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0301-4622(98)00226-9'>10.1016/S0301-4622(98)00226-9</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1667441'>1667441</ext-link>
[15] Cramer C. J., Truhlar D. G., “Implicit solvation models: Equilibria, structure, spectra, and dynamics”, Chem. Rev., 99 (1999), 2161–2200 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/cr960149m'>10.1021/cr960149m</ext-link>
[16] Ponder J. W., Case D. A., “Force fields for protein simulations”, Adv. Prot. Chem., 66 (2003), 27–85 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0065-3233(03)66002-X'>10.1016/S0065-3233(03)66002-X</ext-link>
[17] Chothia C., “Hydrophobic bonding and accessible surface area in proteins”, Nature, 248 (1974), 338–339 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/248338a0'>10.1038/248338a0</ext-link>
[18] Wesson L., Eisenberg D., “Atomic solvation parameters applied to molecular dynamics of proteins in solution”, Prot. Sci., 1 (1992), 227–235 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/pro.5560010204'>10.1002/pro.5560010204</ext-link>
[19] Gallicchio E., Zhang L. Y., Levy R. M., “The SGB/NP hydration free energy model based on the surface generalized Born solvent reaction field and novel nonpolar hydration free energy estimators”, J. Comput. Chem., 23 (2002), 517–529 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/jcc.10045'>10.1002/jcc.10045</ext-link>
[20] Simonson T., “Electrostatics and dynamics of proteins”, Rep. Prog. Phys., 66 (2003), 737–787 <ext-link ext-link-type='doi' href='https://doi.org/10.1088/0034-4885/66/5/202'>10.1088/0034-4885/66/5/202</ext-link>
[21] Baker N. A., “Improving implicit solvent simulations: a Poisson-centric view”, Curr. Opin. Struct. Biol., 15 (2005), 137–143 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/j.sbi.2005.02.001'>10.1016/j.sbi.2005.02.001</ext-link>
[22] Shi X., Koehl P., “The geometry behind numerical solvers of the poisson-boltzmann equation”, Commun. Comput. Phys., 3 (2008), 1032–1050 <ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2445136'>2445136</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1199.82022'>1199.82022</ext-link>
[23] Wang J., Tan C., Tan Y.-H., Lu Q., Luo R., “Poisson–Boltzmann solvents in molecular dynamics simulations”, Commun. Comput. Phys., 3 (2008), 1010–1031
[24] Still W. C., Tempczyk A., Hawley R. C., Hendrickson T., “Semianalytical treatment of solvation for molecular mechanics and dynamics”, J. Am. Chem. Soc., 112 (1990), 6127–6129 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja00172a038'>10.1021/ja00172a038</ext-link>
[25] Ghosh A., Rapp C. S., Friesner R. A., “Generalized Born model based on a surface integral formulation”, J. Phys. Chem. B, 102 (1998), 10983–10990 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/jp982533o'>10.1021/jp982533o</ext-link>
[26] Lide D. R., CRC Handbook of chemistry and physics on CD, CRC-press, Boca Raton, 2005 <ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1114.86306'>1114.86306</ext-link>
[27] Chickos J. S., Acree W. E. Jr., “Enthalpies of sublimation of organic and organometallic compounds. 1910–2001”, J. Phys. Chem. Ref. Data, 31 (2002), 537–698 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1475333'>10.1063/1.1475333</ext-link>
[28] Allen F. H., “The Cambridge Structural Database: a quarter of a million crystal structures and rising”, Acta Cryst. B, 58 (2002), 380–388 <ext-link ext-link-type='doi' href='https://doi.org/10.1107/S0108768102003890'>10.1107/S0108768102003890</ext-link>
[29] Sander R., Compilation of Henry's law constants for inorganic and organic species of potential importance in environmental chemistry (Version 3), , 1999 <ext-link ext-link-type='uri' href='http://www.mpch-mainz.mpg.de/~sander/res/henry.html'>http://www.mpch-mainz.mpg.de/~sander/res/henry.html</ext-link>
[30] Pereyaslavets L. B., Finkelshtein A. V., “Silovoe pole FFSol dlya rascheta vzaimodeistvii molekul v vodnom okruzhenii”, Mol. biol., 44 (2010), 340–354
[31] Landau L. D., Lifshits E. M., Elektrodinamika sploshnykh sred, izd. 2, Nauka, M., 1982 <ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=732443'>732443</ext-link>
[32] Finkelshtein A. V., Ptitsyn O. B., Fizika belka, izd. 3, Knizhnyi dom “Universitet”, M., 2005
[33] Halgren T. A., Damm W., “Polarizable force fields”, Curr. Opin. Struct. Biol., 11 (2001), 236–242 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0959-440X(00)00196-2'>10.1016/S0959-440X(00)00196-2</ext-link>
[34] Finkelstein A. V., “Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding”, Chem. Central J., 1 (2007), 21 <ext-link ext-link-type='doi' href='https://doi.org/10.1186/1752-153X-1-21'>10.1186/1752-153X-1-21</ext-link>
[35] Landau L. D., Lifshits E. M., Kvantovaya mekhanika, chast I, OGIZ, M., L., 1948
[36] Bayly C. I., Cieplak P., Cornell W., Kollman P. A., “A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model”, J. Phys. Chem., 97 (1993), 10269–10280 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/j100142a004'>10.1021/j100142a004</ext-link>
[37] Cornell W. D., Cieplak P., Bayly C. I., Kollman P. A., “Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation”, J. Am. Chem. Soc., 115 (1993), 9620–9631 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja00074a030'>10.1021/ja00074a030</ext-link>
[38] Granovsky A. A., PC GAMESS/Firefly 7.1.E, , 2008, (data obrascheniya: 11.05.2009–06.09.2010) <ext-link ext-link-type='uri' href='http://classic.chem.msu.su/gran/gamess/index.html'>http://classic.chem.msu.su/ gran/gamess/index.html</ext-link>
[39] Schmidt M. W., Baldridge K. K., Boatz J. A., Elbert S. T., Gordon M. S., Jensen J. H., Koseki S., Matsunaga N., Nguyen K. A., Su S., Windus T. L., Dupuis M., Montgomery J. A., “General atomic and molecular electronic structure system”, J. Comput. Chem., 14 (1993), 1347–1363 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/jcc.540141112'>10.1002/jcc.540141112</ext-link>
[40] Wang J., Wang W., Kollman P. A., Case D. A., “Automatic atom type and bond type perception in molecular mechanical calculations”, J. Mol. Graph. Model., 25 (2006), 247–260 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/j.jmgm.2005.12.005'>10.1016/j.jmgm.2005.12.005</ext-link>
[41] Ewig C. S., Thacher T. S., Hagler A. T., “Derivation of Class II force fields. 7. Nonbonded force field parameters for organic compounds”, J. Phys. Chem. B, 103 (1999), 6998–7014 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/jp991011l'>10.1021/jp991011l</ext-link>
[42] Donchev A. G., Galkin N. G., Illarionov A. A., Khoruzhii O. V., Olevanov M. A., Ozrin V. D., Pereyaslavets L. B., Tarasov V. I., “Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase”, J. Comput. Chem., 29 (2008), 1242–1249 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/jcc.20884'>10.1002/jcc.20884</ext-link>