-
1
-
-
14244271476
-
Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
-
DOI 10.1002/1097-0282(2000)56: 4<232::AID-BIP10037>3.0.CO;2-H
-
Cheatham, T.E. III and Young, M.A. (2001) Molecular dynamics simulation of nucleic acids: successes, limitations and promise. Biopolymers, 56, 232-256. (Pubitemid 34105872)
-
(2000)
Biopolymers
, vol.56
, Issue.4
, pp. 232-256
-
-
Cheatham III, T.E.1
Young, M.A.2
-
2
-
-
0242443693
-
Force fields for protein simulations
-
DOI 10.1016/S0065-3233(03)66002-X
-
Ponder, J.W. and Case, D.A. (2003) Force fields for protein simulations. Adv. Prot. Chem., 66, 27-85. (Pubitemid 37392314)
-
(2003)
Advances in Protein Chemistry
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
3
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
DOI 10.1002/prot.21123
-
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A. and Simmerling, C. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Struct. Funct. Bioinf., 65, 712-725. (Pubitemid 44583220)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.3
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
4
-
-
2942532422
-
Development and testing of a general AMBER force field
-
Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A. and Case, D.A. (2004) Development and testing of a general AMBER force field. J. Comput. Chem., 25, 1157-1174.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
5
-
-
0242593434
-
Development and current status of the CHARMM force field for nucleic acids
-
DOI 10.1002/1097-0282(2000)56 :4<257::AID-BIP10029>3.0.CO;2-W
-
MacKerell, A.D. Jr, Banavali, N. and Foloppe, N. (2001) Development and current status of the CHARMM force field for nucleic acids. Biopolymers, 56, 257-265. (Pubitemid 34105873)
-
(2000)
Biopolymers
, vol.56
, Issue.4
, pp. 257-265
-
-
MacKerell Jr., A.D.1
Banavali, N.2
Foloppe, N.3
-
6
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
Mackerell, A.D. Jr, Feig, M. and Brooks, C.L. III (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem., 25, 1400-1415.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1400-1415
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks Iii, C.L.3
-
7
-
-
76249087938
-
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
-
Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I. et al. (2010) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem., 31, 671-690.
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 671-690
-
-
Vanommeslaeghe, K.1
Hatcher, E.2
Acharya, C.3
Kundu, S.4
Zhong, S.5
Shim, J.6
Darian, E.7
Guvench, O.8
Lopes, P.9
Vorobyov, I.10
-
8
-
-
39049147617
-
GLYCAM06: A generalizable biomolecular force field. carbohydrates
-
DOI 10.1002/jcc.20820
-
Kirschner, K.N., Yongye, A.B., Tschampel, S.M., Gonzalez- Outeirino, J., Daniels, C.R., Lachele Foley, B. and Woods, R.J. (2008) GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J. Comput. Chem., 29, 622-655. (Pubitemid 351238844)
-
(2008)
Journal of Computational Chemistry
, vol.29
, Issue.4
, pp. 622-655
-
-
Kirschner, K.N.1
Yongye, A.B.2
Tschampel, S.M.3
Gonzalez-Outeirino, J.4
Daniels, C.R.5
Foley, B.L.6
Woods, R.J.7
-
9
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
DOI 10.1021/ja9621760, PII S0002786396021762
-
Jorgensen, W.L., Maxwell, D.S. and Tirado-Rives, J. (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc., 118, 11225-11236. (Pubitemid 26399746)
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
10
-
-
16444378435
-
On the non-orthogonality problem connected with the use of atomic wave functions in the theory of molecules and crystals
-
Lowdin, P.O. (1950) On the non-orthogonality problem connected with the use of atomic wave functions in the theory of molecules and crystals. J. Chem. Phys., 18, 365-375.
-
(1950)
J. Chem. Phys.
, vol.18
, pp. 365-375
-
-
Lowdin, P.O.1
-
11
-
-
11644266970
-
Electronic population analysis on LCAO-MO molecular wave functions
-
Mulliken, R.S. (1955) Electronic population analysis on LCAO-MO molecular wave functions. I. J. Chem. Phys., 23, 1833-1840.
-
(1955)
I. J. Chem. Phys.
, vol.23
, pp. 1833-1840
-
-
Mulliken, R.S.1
-
12
-
-
0016399124
-
Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals
-
Hagler, A.T., Huler, E. and Lifson, S. (1974) Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J. Am. Chem. Soc., 96, 5319-5327.
-
(1974)
J. Am. Chem. Soc.
, vol.96
, pp. 5319-5327
-
-
Hagler, A.T.1
Huler, E.2
Lifson, S.3
-
13
-
-
0002254462
-
Quantum theory of atoms in molecules-Dalton revisited
-
Bader, R.W.F. and Nguyen-Dang, T.T. (1981) Quantum theory of atoms in molecules-Dalton revisited. Adv. Quantum Chem., 14, 63-124.
-
(1981)
Adv. Quantum Chem.
, vol.14
, pp. 63-124
-
-
Bader, R.W.F.1
Nguyen-Dang, T.T.2
-
14
-
-
33645941402
-
The OPLS [optimized potentials for liquid simulations] potential functions for proteins energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen, W.L. and Tirado-Rives, J. (1988) The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc., 110, 1657-1666.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
15
-
-
0036890178
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
-
DOI 10.1002/jcc.10128
-
Jakalian, A., Jack, D.B. and Bayly, C.I. (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J. Comput. Chem., 23, 1623-1641. (Pubitemid 35330860)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.16
, pp. 1623-1641
-
-
Jakalian, A.1
Jack, D.B.2
Bayly, C.I.3
-
16
-
-
0342877286
-
Determination of partial atomic charges from ab initio molecular electrostatic potentials Application to formamide methanol, and formic acid
-
Momany, F.A. (1978) Determination of partial atomic charges from ab initio molecular electrostatic potentials. Application to formamide, methanol, and formic acid. J. Phys. Chem., 82, 592-601.
-
(1978)
J. Phys. Chem.
, vol.82
, pp. 592-601
-
-
Momany, F.A.1
-
17
-
-
84986513563
-
Representation of the molecular electrostatic potential by a net atomic charge model
-
Cox, S.R. and Williams, D.E. (1981) Representation of the molecular electrostatic potential by a net atomic charge model. J. Comput. Chem., 2, 304-323.
-
(1981)
J. Comput. Chem.
, vol.2
, pp. 304-323
-
-
Cox, S.R.1
Williams, D.E.2
-
18
-
-
84986468608
-
An approach to computing electrostatic charges for molecules
-
Singh, U.C. and Kollman, P.A. (1984) An approach to computing electrostatic charges for molecules. J. Comput. Chem., 5, 129-145.
-
(1984)
J. Comput. Chem.
, vol.5
, pp. 129-145
-
-
Singh, U.C.1
Kollman, P.A.2
-
19
-
-
84988098098
-
Atomic charges derived from electrostatic potentials: A detailed study
-
Chirlian, L.E. and Francl, M.M. (1987) Atomic charges derived from electrostatic potentials: a detailed study. J. Comput. Chem., 8, 894-905.
-
(1987)
J. Comput. Chem.
, vol.8
, pp. 894-905
-
-
Chirlian, L.E.1
Francl, M.M.2
-
20
-
-
84986513567
-
Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis
-
Breneman, C.M. and Wiberg, K.B. (1990) Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J. Comput. Chem., 11, 361-373.
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 361-373
-
-
Breneman, C.M.1
Wiberg, K.B.2
-
21
-
-
0000561939
-
Net atomic charge and multipole models for the Ab initio molecular electric potential
-
Lipkowitz, K.B. and Boyd, D.B. (eds) VCH Publishers, New York
-
Williams, D.E. (1991) Net atomic charge and multipole models for the Ab initio molecular electric potential. In Lipkowitz, K.B. and Boyd, D.B. (eds), Reviews in Computational Chemistry, Vol. 2. VCH Publishers, New York, pp. 219-271.
-
(1991)
Reviews in Computational Chemistry
, vol.2
, pp. 219-271
-
-
Williams, D.E.1
-
22
-
-
84888246185
-
Population analysis and electron densities from quantum mechanics
-
Lipkowitz, K.B. and Boyd, D.B. (eds) VCH Publishers, New York
-
Bachrach, S.M. (1994) Population analysis and electron densities from quantum mechanics. In Lipkowitz, K.B. and Boyd, D.B. (eds), Reviews in Computational Chemistry, Vol. 5. VCH Publishers, New York, pp. 171-227.
-
(1994)
Reviews in Computational Chemistry
, vol.5
, pp. 171-227
-
-
Bachrach, S.M.1
-
23
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: The RESP Model
-
Bayly, C.I., Cieplak, P., Cornell, W.D. and Kollman, P.A. (1993) A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: the RESP Model. J. Phys. Chem., 97, 10269-10280.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
24
-
-
0000667030
-
Application of RESP charges to calculate conformational energies hydrogen bond energies and free energies of solvation
-
Cornell, W.D., Cieplak, P., Bayly, C.I. and Kollman, P.A. (1993) Application of RESP charges to calculate conformational energies, hydrogen bond energies and free energies of solvation. J. Am. Chem. Soc., 115, 9620-9631.
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 9620-9631
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Kollman, P.A.4
-
25
-
-
84986516411
-
Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA RNA and proteins
-
Cieplak, P., Cornell, W.D., Bayly, C.I. and Kollman, P.A. (1995) Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA and proteins. J. Comput. Chem., 16, 1357-1377.
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1357-1377
-
-
Cieplak, P.1
Cornell, W.D.2
Bayly, C.I.3
Kollman, P.A.4
-
26
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
27
-
-
0034604376
-
Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates
-
Woods, R.J. and Chappelle, R. (2000) Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates. J. Mol. Struct.: THEOCHEM, 527, 149-156.
-
(2000)
J. Mol. Struct.: THEOCHEM
, vol.527
, pp. 149-156
-
-
Woods, R.J.1
Chappelle, R.2
-
28
-
-
33846587916
-
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes
-
DOI 10.1002/jcc.20474
-
Mayaan, E., Moser, A., MacKerell, A.D. Jr and York, D.M. (2007) CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. J. Comput. Chem., 28, 495-507. (Pubitemid 46181823)
-
(2007)
Journal of Computational Chemistry
, vol.28
, Issue.2
, pp. 495-507
-
-
Mayaan, E.1
Moser, A.2
Alexander Jr., D.M.3
York, D.M.4
-
29
-
-
67650087533
-
Validating CHARMM parameters and exploring charge distribution models in structure-based drug design
-
Knight, J.L. and Brooks, C.L. III (2009) Validating CHARMM parameters and exploring charge distribution models in structure-based drug design. J. Chem. Theory Comput., 5, 1680-1691.
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1680-1691
-
-
Knight, J.L.1
Brooks Iii, C.L.2
-
30
-
-
0000751110
-
Generation of OPLS-like charges from molecular electrostatic potential using restraints
-
Henchman, R.H. and Essex, J.W. (1999) Generation of OPLS-like charges from molecular electrostatic potential using restraints. J. Comput. Chem., 20, 483-498. (Pubitemid 129652345)
-
(1999)
Journal of Computational Chemistry
, vol.20
, Issue.5
, pp. 483-498
-
-
Henchman, R.H.1
Essex, J.W.2
-
31
-
-
38549152775
-
R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries
-
DOI 10.1093/nar/gkm887
-
Dupradeau, F.-Y., Cezard, C., Lelong, R., Stanislawiak, E., Pecher, J., Delepine, J.C. and Cieplak, P. (2008) R.E.DD.B.: a database for RESP and ESP atomic charges, and force field libraries. Nucleic Acids Res., 36, D360-D367. (Pubitemid 351149749)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Dupradeau, F.-Y.1
Cezard, C.2
Lelong, R.3
Stanislawiak, E.4
Pe5
cher, J.6
Delepine, J.C.7
Cieplak, P.8
-
32
-
-
77954566051
-
The R.E.D. tools: Advances in RESP and ESP charge derivation and force field library building
-
Dupradeau, F.-Y., Pigache, A., Zaffran, T., Savineau, C., Lelong, R., Grivel, N., Lelong, D., Rosanski, W. and Cieplak, P. (2010) The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. Phys. Chem. Chem. Phys., 12, 7821-7839.
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 7821-7839
-
-
Dupradeau, F.-Y.1
Pigache, A.2
Zaffran, T.3
Savineau, C.4
Lelong, R.5
Grivel, N.6
Lelong, D.7
Rosanski, W.8
Cieplak, P.9
-
33
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S. Jr and Weiner, P. (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc., 106, 765-784. (Pubitemid 14548426)
-
(1984)
Journal of the American Chemical Society
, vol.106
, Issue.3
, pp. 765-784
-
-
Weiner Scott, J.1
Kollman Peter, A.2
Case David, A.3
Singh U.Chandra4
Alagona Giuliano5
Profeta Jr., S.6
Weiner Paul7
Ghio Caterina8
-
34
-
-
79952177721
-
-
Gaussian 09, Revision B.1 Inc., Wallingford CT
-
Gaussian 09, Revision B.1, Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V. et al. (2009) Gaussian, Inc., Wallingford CT.
-
(2009)
Gaussian
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Scalmani, G.7
Barone, V.8
-
35
-
-
84893169025
-
General atomic and molecular electronic structure system
-
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. et al. (1993) General atomic and molecular electronic structure system. J. Comput. Chem., 14, 1347-1363.
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 1347-1363
-
-
Schmidt, M.W.1
Baldridge, K.K.2
Boatz, J.A.3
Elbert, S.T.4
Gordon, M.S.5
Jensen, J.H.6
Koseki, S.7
Matsunaga, N.8
Nguyen, K.A.9
Su, S.10
-
36
-
-
33444456362
-
Molecular modeling with the PC GAMESS
-
Nemukhin, A.V., Grigorenko, B.L. and Granovsky, A.A. (2004) Molecular modeling with the PC GAMESS. Moscow Univ. Chem. Bull., 45, 75-102.
-
(2004)
Moscow Univ. Chem. Bull.
, vol.45
, pp. 75-102
-
-
Nemukhin, A.V.1
Grigorenko, B.L.2
Granovsky, A.A.3
-
37
-
-
0004146786
-
-
Royal Society of Chemistry Cambridge
-
Gutsche, C.D. (1989) Calixarenes. Royal Society of Chemistry, Cambridge.
-
(1989)
Calixarenes.
-
-
Gutsche, C.D.1
-
40
-
-
0000538815
-
Analytical molecular surface calculation
-
Connolly, M.L. (1983) Analytical molecular surface calculation. J. Appl. Cryst., 16, 548-558.
-
(1983)
J. Appl. Cryst.
, vol.16
, pp. 548-558
-
-
Connolly, M.L.1
-
41
-
-
23444454552
-
The Amber biomolecular simulation programs
-
DOI 10.1002/jcc.20290
-
Case, D.A., Cheatham, T.E. III, Darden, T., Gohlke, H., Luo, R., Merz, K.M. Jr, Onufriev, A., Simmerling, C., Wang, B. and Woods, R. (2005) The Amber biomolecular simulation programs. J. Comput. Chem., 26, 1668-1688. (Pubitemid 43076180)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
42
-
-
0001253772
-
Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics
-
Dixon, R.W. and Kollman, P.A. (1997) Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics. J. Comput. Chem., 18, 1632-1646.
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1632-1646
-
-
Dixon, R.W.1
Kollman, P.A.2
-
43
-
-
70349087354
-
Polarization effects in molecular mechanical force fields
-
Cieplak, P., Dupradeau, F.-Y., Duan, Y. and Wang, J. (2009) Polarization effects in molecular mechanical force fields. J. Phys.: Condens. Matter, 21, 333102.
-
(2009)
J. Phys.: Condens. Matter
, vol.21
, pp. 333102
-
-
Cieplak, P.1
Dupradeau, F.-Y.2
Duan, Y.3
Wang, J.4
|