-
1
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen, C. B. (1973) Principles that govern the folding of protein chains, Science 181, 223-230.
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
2
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia, C., and Lesk, A. M. (1986) The relation between the divergence of sequence and structure in proteins, EMBO J 5, 823-826.
-
(1986)
EMBO J
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
3
-
-
0032568649
-
A unified statistical framework for sequence comparison and structure comparison
-
DOI 10.1073/pnas.95.11.5913
-
Levitt, M., and Gerstein, M. (1998) A unifi ed statistical framework for sequence comparison and structure comparison, Proc Natl Acad Sci U S A 95, 5913-5920. (Pubitemid 28248939)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.11
, pp. 5913-5920
-
-
Levitt, M.1
Gerstein, M.2
-
4
-
-
0031566432
-
Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation
-
DOI 10.1006/jmbi.1997.1019
-
Russell, R. B., Saqi, M. A., Sayle, R. A., Bates, P. A., and Sternberg, M. J. (1997) Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation, J Mol Biol 269, 423-439. (Pubitemid 27267763)
-
(1997)
Journal of Molecular Biology
, vol.269
, Issue.3
, pp. 423-439
-
-
Russell, R.B.1
Saqi, M.A.S.2
Sayle, R.A.3
Bates, P.A.4
Sternberg, M.J.E.5
-
5
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell Jr., A. D., Bashford, D., Bellott, M., Dunbrack Jr., R. L., 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 III, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wlorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins, J Phys Chem B 102, 3586-3616. (Pubitemid 128576688)
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
6
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fi elds: 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., 3rd. (2004) Extending the treatment of backbone energetics in protein force fi elds: 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, C.L.3
-
7
-
-
0029011701
-
A second generation force field for the simulation of proteins nucleic acids, and organic molecules
-
Cornell, W. D., P., C., Bayley, C. I., Gould, I. R., Merz Jr., 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
Bayley, C.I.2
Gould, I.R.3
Merz Jr., K.M.4
Ferguson, D.M.5
Spellmeyer, D.C.6
Fox, T.7
Caldwell, J.W.8
Kollman, P.A.9
-
8
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformation energies of organic and biological molecules?
-
Wang, J., Cieplak, P., and Kollman, P. A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformation energies of organic and biological molecules?, J Comput Chem 21, 1049-1074.
-
(2000)
J Comput Chem
, vol.21
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
9
-
-
0242663237
-
A point-charge force fi eld for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., and Kollman, P. (2003) A point-charge force fi eld for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J Comput Chem 24, 1999-2012.
-
(2003)
J Comput Chem
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
10
-
-
4444282928
-
A biomolecular force fi eld based on the free enthalpy of hydration and solvation: The GROMOS force-fi eld parameter sets 53A5 and 53A6
-
Oostenbrink, C., Villa, A., Mark, A. E., and van Gunsteren, W. F. (2004) A biomolecular force fi eld based on the free enthalpy of hydration and solvation: the GROMOS force-fi eld parameter sets 53A5 and 53A6, J Comput Chem 25, 1656-1676.
-
(2004)
J Comput Chem
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
Van Gunsteren, W.F.4
-
11
-
-
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 fi eld 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
-
12
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
Brooks, B. R., Brooks, C. L., 3rd, Mackerell, A. D., Jr., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Cafl isch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R. W., Post, C. B., Pu, J. Z., Schaefer, M., Tidor, B., Venable, R. M., Woodcock, H. L., Wu, X., Yang, W., York, D. M., and Karplus, M. (2009) CHARMM: the biomolecular simulation program, J Comput Chem 30, 1545-1614.
-
(2009)
J Comput Chem
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks, C.L.2
Mackerell Jr., A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Cafl Isch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
13
-
-
23444454552
-
The Amber biomolecular simulation programs
-
DOI 10.1002/jcc.20290
-
Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., Onufriev, A., Simmerling, C., Wang, B., and Woods, R. J. (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
-
14
-
-
30444448249
-
The GROMOS software for biomolecular simulation: GROMOS05
-
DOI 10.1002/jcc.20303
-
Christen, M., Hunenberger, P. H., Bakowies, D., Baron, R., Burgi, R., Geerke, D. P., Heinz, T. N., Kastenholz, M. A., Krautler, V., Oostenbrink, C., Peter, C., Trzesniak, D., and van Gunsteren, W. F. (2005) The GROMOS software for biomolecular simulation: GROMOS05, J Comput Chem 26, 1719-1751. (Pubitemid 43076183)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1719-1751
-
-
Christen, M.1
Hunenberger, P.H.2
Bakowies, D.3
Baron, R.4
Burgi, R.5
Geerke, D.P.6
Heinz, T.N.7
Kastenholz, M.A.8
Krautler, V.9
Oostenbrink, C.10
Peter, C.11
Trzesniak, D.12
Van Gunsteren, W.F.13
-
15
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
DOI 10.1002/jcc.20289
-
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, 1781-1802. (Pubitemid 43078511)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
16
-
-
46249092554
-
GROMACS 4: Algorithms or highly effi cient load-balanced, and scalable molecular simulation
-
Hess, B., Kutzner, C., van der Spoel, D., and Lindahl, E. (2008) GROMACS 4: Algorithms or highly effi cient, load-balanced, and scalable molecular simulation, J Chem Theory Comput 4, 435-447.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
17
-
-
34548283148
-
Scalable algorithms for molecular dynamics simulations on commodity clusters
-
ACM, Tampa, FL
-
Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., and Shaw, D. E. (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters, in ACM/IEEE Conference on Supercomputing (SC06), ACM, Tampa, FL.
-
(2006)
ACM/IEEE Conference on Supercomputing (SC06)
-
-
Bowers, K.J.1
Chow, E.2
Xu, H.3
Dror, R.O.4
Eastwood, M.P.5
Gregersen, B.A.6
Klepeis, J.L.7
Kolossvary, I.8
Moraes, M.A.9
Sacerdoti, F.D.10
Salmon, J.K.11
Shan, Y.12
Shaw, D.E.13
-
19
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
DOI 10.1006/jmbi.1993.1626
-
Sali, A., and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints, J Mol Biol 234, 779-815. (Pubitemid 24007801)
-
(1993)
Journal of Molecular Biology
, vol.234
, Issue.3
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
20
-
-
49649114605
-
Protein structure modeling with MODELLER
-
Eswar, N., Eramian, D., Webb, B., Shen, M. Y., and Sali, A. (2008) Protein structure modeling with MODELLER, Methods Mol Biol 426, 145-159.
-
(2008)
Methods Mol Biol
, vol.426
, pp. 145-159
-
-
Eswar, N.1
Eramian, D.2
Webb, B.3
Shen, M.Y.4
Sali, A.5
-
21
-
-
0042622380
-
SWISS-MODEL: An automated protein homology-modeling server
-
DOI 10.1093/nar/gkg520
-
Schwede, T., Kopp, J., Guex, N., and Peitsch, M. C. (2003) SWISS-MODEL: An automated protein homology-modeling server, Nucleic Acids Res 31, 3381-3385. (Pubitemid 37442164)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3381-3385
-
-
Schwede, T.1
Kopp, J.2
Guex, N.3
Peitsch, M.C.4
-
22
-
-
0001546949
-
The classical equation of state of gaseous helium neon, and argon
-
Buckingham, R. A. (1938) The classical equation of state of gaseous helium, neon, and argon, Proc R Soc Lond. A 168, 264-283.
-
(1938)
Proc R Soc Lond. A
, vol.168
, pp. 264-283
-
-
Buckingham, R.A.1
-
23
-
-
0034718590
-
Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities
-
Avbelj, F., Luo, P., and Baldwin, R. L. (2000) Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities, Proc Natl Acad Sci U S A 97, 10786-10791.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 10786-10791
-
-
Avbelj, F.1
Luo, P.2
Baldwin, R.L.3
-
24
-
-
0030736114
-
Free energy of amide hydrogen bond formation in vacuum, in water, and in liquid alkane solution
-
Ben-Tal, N., Sitkoff, D., Topol, I. A., Yang, A. S., Burt, S. K., and Honig, B. (1997) Free energy of amide hydrogen bond formation in vacuum, in water, and in liquid alkane solution, J Phys Chem B 101, 450-457. (Pubitemid 127617329)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.3
, pp. 450-457
-
-
Ben-Tal, N.1
Sitkoff, D.2
Topol, I.A.3
Yang, A.-S.4
Burt, S.K.5
Honig, B.6
-
25
-
-
0242363173
-
Energetics of hydrogen bonds in peptides
-
DOI 10.1073/pnas.2133366100
-
Sheu, S. Y., Yang, D. Y., Selzle, H. L., and Schlag, E. W. (2003) Energetics of hydrogen bonds in peptides, Proc Natl Acad Sci U S A 100, 12683-12687. (Pubitemid 37339959)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.22
, pp. 12683-12687
-
-
Sheu, S.-Y.1
Yang, D.-Y.2
Selzle, H.L.3
Schlag, E.W.4
-
26
-
-
0002162214
-
On the electrostatic directionality of N-H.O=C hydrogen bonding
-
Mitchell, J. B. O., and Price, S. L. (1989) On the electrostatic directionality of N-H.O=C hydrogen bonding, Chem Phys Lett 154, 267-272.
-
(1989)
Chem Phys Lett
, vol.154
, pp. 267-272
-
-
Mitchell, J.B.O.1
Price, S.L.2
-
27
-
-
77950131426
-
Development of a polarizable force fi eld using multiple fl uctuating charges per atom
-
Zhao, D. X., Liu, C., Wang, F. F., Yu, C. Y., Gong, L. D., Liu, S. B., and Yang, Z. Z. (2010) Development of a polarizable force fi eld using multiple fl uctuating charges per atom, J Chem Theory Comput 6, 795-804.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 795-804
-
-
Zhao, D.X.1
Liu, C.2
Wang, F.F.3
Yu, C.Y.4
Gong, L.D.5
Liu, S.B.6
Yang, Z.Z.7
-
28
-
-
33847799937
-
Conformational analysis. Application of the molecular-mechanics method to alcohols and ethers
-
Allinger, N. L., and Chung, D. Y. (1976) Conformational analysis. Application of the molecular-mechanics method to alcohols and ethers, J Am Chem Soc 98, 6798-6803.
-
(1976)
J Am Chem Soc
, vol.98
, pp. 6798-6803
-
-
Allinger, N.L.1
Chung, D.Y.2
-
29
-
-
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
-
30
-
-
0000051486
-
Derivation of force fi elds for molecular mechanics and dynamics from ab initio energy surfaces
-
Maple, J. R., Dinur, U., and Hagler, A. T. (1988) Derivation of force fi elds for molecular mechanics and dynamics from ab initio energy surfaces, Proc Natl Acad Sci U S A 85, 5350-5354.
-
(1988)
Proc Natl Acad Sci U S A
, vol.85
, pp. 5350-5354
-
-
Maple, J.R.1
Dinur, U.2
Hagler, A.T.3
-
31
-
-
84986527718
-
Derivation of class II force fi elds. Methodology and quantum force fi eld for the alkyl functional group and alkane molecules
-
Maple, J. R., Hwang, M. J., Stockfi sch, T. P., Dinur, U., Waldman, M., Ewig, C. S., and Hagler, A. T. (1994) Derivation of class II force fi elds. Methodology and quantum force fi eld for the alkyl functional group and alkane molecules, J Comput Chem 15, 162-182.
-
(1994)
J Comput Chem
, vol.15
, pp. 162-182
-
-
Maple, J.R.1
Hwang, M.J.2
Stockfi Sch, T.P.3
Dinur, U.4
Waldman, M.5
Ewig, C.S.6
Hagler, A.T.7
-
32
-
-
0029976427
-
Statistical potentials extracted from protein structures: How accurate are they?
-
DOI 10.1006/jmbi.1996.0175
-
Thomas, P. D., and Dill, K. A. (1996) Statistical potentials extracted from protein structures: how accurate are they?, J Mol Biol 257, 457-469. (Pubitemid 26114046)
-
(1996)
Journal of Molecular Biology
, vol.257
, Issue.2
, pp. 457-469
-
-
Thomas, P.D.1
Dill, K.A.2
-
33
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
DOI 10.1006/jmbi.1997.0959
-
Simons, K. T., Kooperberg, C., Huang, E., and Baker, D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions, J Mol Biol 268, 209-225. (Pubitemid 27192690)
-
(1997)
Journal of Molecular Biology
, vol.268
, Issue.1
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
34
-
-
77950823568
-
Orientation-dependent backbone-only residue pair scoring functions for fi xed backbone protein design
-
Bordner, A. J. (2010) Orientation-dependent backbone-only residue pair scoring functions for fi xed backbone protein design, Bmc Bioinformatics 11, 192.
-
(2010)
Bmc Bioinformatics
, vol.11
, pp. 192
-
-
Bordner, A.J.1
-
35
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
DOI 10.1110/ps.0217002
-
Zhou, H., and Zhou, Y. (2002) Distancescaled, fi nite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction, Protein Sci 11, 2714-2726. (Pubitemid 35191145)
-
(2002)
Protein Science
, vol.11
, Issue.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
36
-
-
46449139781
-
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions
-
DOI 10.1110/ps.033480.107
-
Yang, Y., and Zhou, Y. (2008) Ab initio folding of terminal segments with secondary structures reveals the fi ne difference between two closely related all-atom statistical energy functions, Protein Sci 17, 1212-1219. (Pubitemid 351930918)
-
(2008)
Protein Science
, vol.17
, Issue.7
, pp. 1212-1219
-
-
Yang, Y.1
Zhou, Y.2
-
37
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
DOI 10.1110/ps.062416606
-
Shen, M. Y., and Sali, A. (2006) Statistical potential for assessment and prediction of protein structures, Protein Sci 15, 2507-2524. (Pubitemid 44771688)
-
(2006)
Protein Science
, vol.15
, Issue.11
, pp. 2507-2524
-
-
Shen, M.-Y.1
Sali, A.2
-
38
-
-
70450106216
-
Improved prediction of protein side-chain conformations with SCWRL4
-
Krivov, G. G., Shapovalov, M. V., and Dunbrack, R. L., Jr. (2009) Improved prediction of protein side-chain conformations with SCWRL4, Proteins 77, 778-795.
-
(2009)
Proteins
, vol.77
, pp. 778-795
-
-
Krivov, G.G.1
Shapovalov, M.V.2
Dunbrack Jr., R.L.3
-
39
-
-
84986522918
-
ICM-A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
-
Abagyan, R., Totrov, M., and Kuznetsov, D. (1994) ICM-A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation, J Comput Chem 15, 488-506.
-
(1994)
J Comput Chem
, vol.15
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kuznetsov, D.3
-
40
-
-
5944250450
-
Energy parameters in polypeptides. VII. Geometric parameters partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials or the naturally occurring amino acids
-
Momany, F. A., McGuire, R. F., Burgess, A. W., and Scheraga, H. A. (1975) Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials or the naturally occurring amino acids, J Phys Chem 79, 2361-2381.
-
(1975)
J Phys Chem
, vol.79
, pp. 2361-2381
-
-
Momany, F.A.1
McGuire, R.F.2
Burgess, A.W.3
Scheraga, H.A.4
-
41
-
-
33845550595
-
Energy parameters in polypeptides. Updating of geometric parameters nonbonded interactions and hydrogen bond interactions for the naturally occurring amino acids
-
Nemethy, G., Pottle, M. S., and Scheraga, H. A. (1983) Energy parameters in polypeptides. Updating of geometric parameters, nonbonded interactions and hydrogen bond interactions for the naturally occurring amino acids, J Phys Chem 87, 1883-1887.
-
(1983)
J Phys Chem
, vol.87
, pp. 1883-1887
-
-
Nemethy, G.1
Pottle, M.S.2
Scheraga, H.A.3
-
42
-
-
0001731773
-
Energy parameters in polypeptides. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm with application to proline-containing peptides
-
Nemethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S., and Scheraga, H. A. (1992) Energy parameters in polypeptides. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides, J Phys Chem 96, 6472-6484.
-
(1992)
J Phys Chem
, vol.96
, pp. 6472-6484
-
-
Nemethy, G.1
Gibson, K.D.2
Palmer, K.A.3
Yoon, C.N.4
Paterlini, G.5
Zagari, A.6
Rumsey, S.7
Scheraga, H.A.8
-
43
-
-
33645511814
-
A new force fi eld (ECEPP-05) for peptides proteins and organic molecules
-
Arnautova, Y. A., Jagielska, A., and Scheraga, H. A. (2006) A new force fi eld (ECEPP-05) for peptides, proteins, and organic molecules, J Phys Chem B 110, 5025-5044.
-
(2006)
J Phys Chem B
, vol.110
, pp. 5025-5044
-
-
Arnautova, Y.A.1
Jagielska, A.2
Scheraga, H.A.3
-
44
-
-
78650798307
-
Development of a new physics-based internal coordinate mechanics force fi eld and its application to protein loop modeling
-
Arnautova, Y. A., Abagyan, R. A., and Totrov, M. (2011) Development of a new physics-based internal coordinate mechanics force fi eld and its application to protein loop modeling, Proteins 79, 477-498.
-
(2011)
Proteins
, vol.79
, pp. 477-498
-
-
Arnautova, Y.A.1
Abagyan, R.A.2
Totrov, M.3
-
45
-
-
0033135638
-
Effective energy function for proteins in solution
-
DOI 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N
-
Lazaridis, T., and Karplus, M. (1999) Effective energy function for proteins in solution, Proteins 35, 133-152. (Pubitemid 29165128)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.35
, Issue.2
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
46
-
-
2342593131
-
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
-
DOI 10.1073/pnas.0307578101
-
Morozov, A. V., Kortemme, T., Tsemekhman, K., and Baker, D. (2004) Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations, Proc Natl Acad Sci U S A 101, 6946-6951. (Pubitemid 38596423)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.18
, pp. 6946-6951
-
-
Morozov, A.V.1
Kortemme, T.2
Tsemekhman, K.3
Baker, D.4
-
47
-
-
0035974484
-
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
-
DOI 10.1002/jcc.1065
-
Cieplak, P., Caldwell, J., and Kollman, P. (2001) Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/ water partition coeffi cients of the nucleic acid bases, J Comput Chem 22, 1048-1057. (Pubitemid 32614376)
-
(2001)
Journal of Computational Chemistry
, vol.22
, Issue.10
, pp. 1048-1057
-
-
Cieplak, P.1
Caldwell, J.2
Kollman, P.3
-
48
-
-
77749298172
-
Current status of the AMOEBA polarizable force fi eld
-
Ponder, J. W., Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., Lambrecht, D. S., DiStasio, R. A., Jr., Head-Gordon, M., Clark, G. N., Johnson, M. E., and Head-Gordon, T. Current status of the AMOEBA polarizable force fi eld, J Phys Chem B 114, 2549-2564.
-
J Phys Chem B
, vol.114
, pp. 2549-2564
-
-
Ponder, J.W.1
Wu, C.2
Ren, P.3
Pande, V.S.4
Chodera, J.D.5
Schnieders, M.J.6
Haque, I.7
Mobley, D.L.8
Lambrecht, D.S.9
DiStasio Jr., R.A.10
Head-Gordon, M.11
Clark, G.N.12
Johnson, M.E.13
Head-Gordon, T.14
-
49
-
-
0036882094
-
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests
-
DOI 10.1002/jcc.10125
-
Kaminski, G. A., Stern, H. A., Berne, B. J., Friesner, R. A., Cao, Y. X., Murphy, R. B., Zhou, R., and Halgren, T. A. (2002) Development of a polarizable force fi eld for proteins via ab initio quantum chemistry: First generation model and gas phase tests, J Comput Chem 23, 1515-1531. (Pubitemid 35330854)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.16
, pp. 1515-1531
-
-
Kaminski, G.A.1
Stern, H.A.2
Berne, B.J.3
Friesner, R.A.4
Cao, Y.X.5
Murphy, R.B.6
Zhou, R.7
Halgren, T.A.8
-
50
-
-
0347655649
-
CHARMM fl uctuating charge force fi eld for proteins: I parameterization and application to bulk organic liquid simulations
-
Patel, S., and Brooks, C. L., 3rd. (2004) CHARMM fl uctuating charge force fi eld for proteins: I parameterization and application to bulk organic liquid simulations, J Comput Chem 25, 1-15.
-
(2004)
J Comput Chem
, vol.25
, pp. 1-15
-
-
Patel, S.1
Brooks, C.L.2
-
51
-
-
4043057278
-
CHARMM fl uctuating charge force fi eld for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
-
Patel, S., Mackerell, A. D., Jr., and Brooks, C. L., 3 rd. (2004) CHARMM fl uctuating charge force fi eld for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model, J Comput Chem 25, 1504-1514.
-
(2004)
J Comput Chem
, vol.25
, pp. 1504-1514
-
-
Patel, S.1
Mackerell Jr., A.D.2
Brooks, C.L.3
-
52
-
-
0041878923
-
Modeling induced with classical Drude Oscillators: Theory and molecular dynamics simulation algorithm
-
Lamoureux, G., and Roux, B. (2003) Modeling induced with classical Drude Oscillators: Theory and molecular dynamics simulation algorithm, J Chem Phys 119, 245-249.
-
(2003)
J Chem Phys
, vol.119
, pp. 245-249
-
-
Lamoureux, G.1
Roux, B.2
-
53
-
-
30344482264
-
A polarizable model of water for molecular dynamics simulations of biomolecules
-
DOI 10.1016/j.cplett.2005.10.135, PII S0009261405017069
-
Lamoureux, G., Harder, E., Vorobyov, I. V., Roux, B., and MacKerell, A. D. (2006) A polarizable model of water for molecular dynamics simulations of biomolecules, Chem Phys Lett 418, 245-249. (Pubitemid 43063383)
-
(2006)
Chemical Physics Letters
, vol.418
, Issue.1-3
, pp. 245-249
-
-
Lamoureux, G.1
Harder, E.2
Vorobyov, I.V.3
Roux, B.4
MacKerell Jr., A.D.5
-
54
-
-
0017187836
-
The nature of the accessible and buried surfaces in proteins
-
Chothia, C. (1976) The nature of the accessible and buried surfaces in proteins, J Mol Biol 105, 1-12.
-
(1976)
J Mol Biol
, vol.105
, pp. 1-12
-
-
Chothia, C.1
-
55
-
-
0017884417
-
The hydrophobic effect and the organization of living matter
-
Tanford, C. (1978) The hydrophobic effect and the organization of living matter, Science 200, 1012-1018. (Pubitemid 8346922)
-
(1978)
Science
, vol.200
, Issue.4345
, pp. 1012-1018
-
-
Tanford, C.1
-
56
-
-
0021049880
-
Waterlogged molecules
-
Wolfenden, R. (1983) Waterlogged molecules, Science 222, 1087-1093. (Pubitemid 14203776)
-
(1983)
Science
, vol.222
, Issue.4628
, pp. 1087-1093
-
-
Wolfenden, R.1
-
57
-
-
0036836445
-
A reappraisal of what we have learnt during three decades of computer simulations on water
-
Guillot, B. (2002) A reappraisal of what we have learnt during three decades of computer simulations on water, J Mol Liq 101, 219-260.
-
(2002)
J Mol Liq
, vol.101
, pp. 219-260
-
-
Guillot, B.1
-
58
-
-
1242346370
-
The missing term in effective pair potentials
-
Berendsen, H. J. C., Grigera, J. R., and Straatsma, T. P. (1987) The missing term in effective pair potentials, J Phys Chem 91, 6269-6271.
-
(1987)
J Phys Chem
, vol.91
, pp. 6269-6271
-
-
Berendsen, H.J.C.1
Grigera, J.R.2
Straatsma, T.P.3
-
59
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water, J Chem Phys 79, 926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
60
-
-
84906391926
-
Temperature and size dependence for Monte Carlo simulations of TIP4P water
-
Jorgensen, W. L., and Madura, J. D. (1985) Temperature and size dependence for Monte Carlo simulations of TIP4P water, Mol Phys 56, 1381-1380.
-
(1985)
Mol Phys
, vol.56
, pp. 1381-1380
-
-
Jorgensen, W.L.1
Madura, J.D.2
-
61
-
-
0034831674
-
Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model
-
DOI 10.1063/1.1336805
-
Rick, S. W. (2001) Simulations of ice and liquid water over a range of temperatures using the fl uctuating charge model, J Chem Phys 114, 2276-2283. (Pubitemid 32873150)
-
(2001)
Journal of Chemical Physics
, vol.114
, Issue.5
, pp. 2276-2283
-
-
Rick, S.W.1
-
62
-
-
0001624472
-
Molecular dynamics simulation of dielectric properties of water
-
Anderson, J., Ullo, J. J., and S., Y. (1987) Molecular dynamics simulation of dielectric properties of water, J Chem Phys 87, 1726-1732.
-
(1987)
J Chem Phys
, vol.87
, pp. 1726-1732
-
-
Anderson, J.1
Ullo, J.J.2
-
63
-
-
0001251663
-
Molecular-dynamics study of atomic motions in water
-
Toukan, K., and Rahman, A. (1985) Molecular-dynamics study of atomic motions in water, Phys Rev B 31, 2643-2648.
-
(1985)
Phys Rev B
, vol.31
, pp. 2643-2648
-
-
Toukan, K.1
Rahman, A.2
-
64
-
-
0035451052
-
What are the dielectric "constants" of proteins and how to validate electrostatic models?
-
DOI 10.1002/prot.1106
-
Schutz, C. N., and Warshel, A. (2001) What are the dielectric constants of proteins and how to validate electrostatic models?, Proteins 44, 400-417. (Pubitemid 32768578)
-
(2001)
Proteins: Structure, Function and Genetics
, vol.44
, Issue.4
, pp. 400-417
-
-
Schutz, C.N.1
Warshel, A.2
-
65
-
-
0029833446
-
Charge screening and the dieletric constant of proteins: Insights from molecular dynamics
-
DOI 10.1021/ja960884f
-
Simonson, T., and Brooks III, C. D. (1996) Charge screening and the dielectric constant of proteins: Insights from molecular mechanics, J Am Chem Soc 118, 8452-8458. (Pubitemid 26305268)
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.35
, pp. 8452-8458
-
-
Simonson, T.1
Brooks III, C.L.2
-
66
-
-
0037080244
-
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
-
DOI 10.1002/jcc.1161
-
Rocchia, W., Sridharan, S., Nicholls, A., Alexov, E., Chiabrera, A., and Honig, B. (2002) Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction fi eld energies: applications to the molecular systems and geometric objects, J Comput Chem 23, 128-137. (Pubitemid 34063137)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.1
, pp. 128-137
-
-
Rocchia, W.1
Sridharan, S.2
Nicholls, A.3
Alexov, E.4
Chiabrera, A.5
Honig, B.6
-
68
-
-
0035971738
-
A smooth permittivity function for Poisson-Boltzmann solvation methods
-
DOI 10.1002/jcc.1032
-
Grant, J. A., Pickup, B. T., and Nicholls, A. (2001) A smooth permittivity function for Poisson-Boltzmann solvation methods, J Comput Chem 22, 608-640. (Pubitemid 32382607)
-
(2001)
Journal of Computational Chemistry
, vol.22
, Issue.6
, pp. 608-640
-
-
Grant, J.A.1
-
70
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
DOI 10.1073/pnas.181342398
-
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 U S A 98, 10037-10041. (Pubitemid 32802969)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.18
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
72
-
-
0034863617
-
Rapid boundary element solvation electrostatics calculations in folding simulations: Successful folding of a 23-residue peptide
-
DOI 10.1002/1097-0282(2001)60:2<124::AID-BIP1008>3.0.CO;2-S
-
Totrov, M., and Abagyan, R. (2001) Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide, Biopolymers 60, 124-133. (Pubitemid 32743529)
-
(2001)
Biopolymers - Peptide Science Section
, vol.60
, Issue.2
, pp. 124-133
-
-
Totrov, M.1
Abagyan, R.2
-
73
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W. C., Tempczyk, A., Hawley, R. C., and Hendrickson, T. (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics, J Am Chem Soc 112, 6127-6129.
-
(1990)
J Am Chem Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
74
-
-
0033654297
-
Generalized born models of macromolecular solvation effects
-
Bashford, D., and Case, D. A. (2000) Generalized born models of macromolecular solvation effects, Annu Rev Phys Chem 51, 129-152.
-
(2000)
Annu Rev Phys Chem
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
75
-
-
0002636134
-
Pairwise Solute Descreening of Solute Charges from a Dielectric Medium
-
Hawkins, G. D., Cramer, C. J., and Truhlar, D. G. (1995) Pairwise Solute Descreening of Solute Charges from a Dielectric Medium, Chemical Physics Letters 246, 122-129.
-
(1995)
Chemical Physics Letters
, vol.246
, pp. 122-129
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
76
-
-
33748390341
-
Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
-
Hawkins, G. D., Cramer, C. J., and Truhlar, D. G. (1996) Parameterized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium, J Phys Chem 100, 19824-19839. (Pubitemid 126786901)
-
(1996)
Journal of Physical Chemistry
, vol.100
, Issue.51
, pp. 19824-19839
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
77
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
-
Qiu, D., Shenkin, P. S., Hollinger, F. P., and Still, W. C. (1997) The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii, Journal of Physical Chemistry A 101, 3005-3014. (Pubitemid 127580882)
-
(1997)
Journal of Physical Chemistry A
, vol.101
, Issue.16
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
78
-
-
0016352763
-
Hydrophobic bonding and accessible surface area in proteins
-
Chothia, C. (1974) Hydrophobic bonding and accessible surface area in proteins, Nature 248, 338-339.
-
(1974)
Nature
, vol.248
, pp. 338-339
-
-
Chothia, C.1
-
79
-
-
0017429069
-
Areas volumes, packing and protein structure
-
Richards, F. M. (1977) Areas, volumes, packing and protein structure, Annu Rev Biophys Bioeng 6, 151-176.
-
(1977)
Annu Rev Biophys Bioeng
, vol.6
, pp. 151-176
-
-
Richards, F.M.1
-
80
-
-
84986534141
-
A rapid method for calculating derivatives of solvent accessible surface areas of molecules
-
Sridharan, S., Nicholls, A., and Sharp, K. A. (2004) A rapid method for calculating derivatives of solvent accessible surface areas of molecules, J Comput Chem 16, 1038-1044.
-
(2004)
J Comput Chem
, vol.16
, pp. 1038-1044
-
-
Sridharan, S.1
Nicholls, A.2
Sharp, K.A.3
-
81
-
-
0021755764
-
Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect
-
Richmond, T. J. (1984) Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect, J Mol Biol 178, 63-89.
-
(1984)
J Mol Biol
, vol.178
, pp. 63-89
-
-
Richmond, T.J.1
-
82
-
-
0027080909
-
Atomic solvation parameters applied to molecular dynamics of proteins in solution
-
Wesson, L., and Eisenberg, D. (1992) Atomic solvation parameters applied to molecular dynamics of proteins in solution, Protein Sci 1, 227-235. (Pubitemid 23007289)
-
(1992)
Protein Science
, vol.1
, Issue.2
, pp. 227-235
-
-
Wesson, L.1
Eisenberg, D.2
-
83
-
-
0036138028
-
Evaluation of a fast implicit solvent model for molecular dynamics simulations
-
DOI 10.1002/prot.10001
-
Ferrara, P., Apostolakis, J., and Cafl isch, A. (2002) Evaluation of a fast implicit solvent model for molecular dynamics simulations, Proteins 46, 24-33. (Pubitemid 34033573)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.46
, Issue.1
, pp. 24-33
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
84
-
-
0031954925
-
Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
-
Wallin, E., and von Heijne, G. (1998) Genomewide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms, Protein Sci 7, 1029-1038. (Pubitemid 28216544)
-
(1998)
Protein Science
, vol.7
, Issue.4
, pp. 1029-1038
-
-
Wallin, E.1
Von Heijne, G.2
-
85
-
-
60149096311
-
Properties and identifi cation of human protein drug targets
-
Bakheet, T. M., and Doig, A. J. (2009) Properties and identifi cation of human protein drug targets, Bioinformatics 25, 451-457.
-
(2009)
Bioinformatics
, vol.25
, pp. 451-457
-
-
Bakheet, T.M.1
Doig, A.J.2
-
86
-
-
35148838537
-
Drugtarget network
-
Yildirim, M. A., Goh, K. I., Cusick, M. E., Barabasi, A. L., and Vidal, M. (2007) Drugtarget network, Nat Biotechnol 25, 1119-1126.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 1119-1126
-
-
Yildirim, M.A.1
Goh, K.I.2
Cusick, M.E.3
Barabasi, A.L.4
Vidal, M.5
-
87
-
-
34249981222
-
Determining membrane protein structures: Still a challenge!
-
DOI 10.1016/j.tibs.2007.04.001, PII S0968000407000849
-
Lacapere, J. J., Pebay-Peyroula, E., Neumann, J. M., and Etchebest, C. (2007) Determining membrane protein structures: still a challenge!, Trends Biochem Sci 32, 259-270. (Pubitemid 46881229)
-
(2007)
Trends in Biochemical Sciences
, vol.32
, Issue.6
, pp. 259-270
-
-
Lacapere, J.-J.1
Pebay-Peyroula, E.2
Neumann, J.-M.3
Etchebest, C.4
-
88
-
-
34548133239
-
P-glycoprotein models of the apo and ATP-bound states based on homology with Sav1866 and MalK
-
DOI 10.1016/j.febslet.2007.07.069, PII S0014579307008393
-
O'Mara, M. L., and Tieleman, D. P. (2007) P-glycoprotein models of the apo and ATPbound states based on homology with Sav1866 and MalK, FEBS Lett 581, 4217-4222. (Pubitemid 47301854)
-
(2007)
FEBS Letters
, vol.581
, Issue.22
, pp. 4217-4222
-
-
O'Mara, M.L.1
Tieleman, D.P.2
-
89
-
-
77954052042
-
Homology modeling of G-protein-coupled receptors with X-ray structures on the rise
-
Yarnitzky, T., Levit, A., and Niv, M. Y. (2010) Homology modeling of G-protein-coupled receptors with X-ray structures on the rise, Curr Opin Drug Discov Devel 13, 317-325.
-
(2010)
Curr Opin Drug Discov Devel
, vol.13
, pp. 317-325
-
-
Yarnitzky, T.1
Levit, A.2
Niv, M.Y.3
-
90
-
-
77954052042
-
Homology modeling of G-protein-coupled receptors with X-ray structures on the rise
-
Yarnitzky, T., Levit, A., and Niv, M. Y. Homology modeling of G-protein-coupled receptors with X-ray structures on the rise, Curr Opin Drug Discov Devel 13, 317-325.
-
Curr Opin Drug Discov Devel
, vol.13
, pp. 317-325
-
-
Yarnitzky, T.1
Levit, A.2
Niv, M.Y.3
-
91
-
-
0037194983
-
Introducing an implicit membrane in generalized born/solvent accessibility continuum solvent models
-
DOI 10.1021/jp020674r
-
Spassov, V. Z., Yan, L., and Szalma, S. (2002) Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models, J Phys Chem B 106, 8726-8738. (Pubitemid 35382883)
-
(2002)
Journal of Physical Chemistry B
, vol.106
, Issue.34
, pp. 8726-8738
-
-
Spassov, V.Z.1
Yan, L.2
Szalma, S.3
-
92
-
-
0038675609
-
Effective energy function for proteins in lipid membranes
-
DOI 10.1002/prot.10410
-
Lazaridis, T. (2003) Effective energy function for proteins in lipid membranes, Proteins 52, 176-192. (Pubitemid 36828942)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.52
, Issue.2
, pp. 176-192
-
-
Lazaridis, T.1
-
93
-
-
18144394277
-
Are acidic and basic groups in buried proteins predicted to be ionized?
-
DOI 10.1016/j.jmb.2005.03.051
-
Kim, J., Mao, J., and Gunner, M. R. (2005) Are acidic and basic groups in buried proteins predicted to be ionized?, J Mol Biol 348, 1283-1298. (Pubitemid 40613020)
-
(2005)
Journal of Molecular Biology
, vol.348
, Issue.5
, pp. 1283-1298
-
-
Kim, J.1
Mao, J.2
Gunner, M.R.3
-
94
-
-
23144457576
-
as and adding missing hydrogens to macromolecules
-
DOI 10.1093/nar/gki464
-
Gordon, J. C., Myers, J. B., Folta, T., Shoja, V., Heath, L. S., and Onufriev, A. (2005) H++: a server for estimating pKas and adding missing hydrogens to macromolecules, Nucleic Acids Res 33, W368-371. (Pubitemid 44529945)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Gordon, J.C.1
Myers, J.B.2
Folta, T.3
Shoja, V.4
Heath, L.S.5
Onufriev, A.6
-
95
-
-
28644432877
-
a values
-
DOI 10.1002/prot.20660
-
Li, H., Robertson, A. D., and Jensen, J. H. (2005) Very fast empirical prediction and rationalization of protein pKa values, Proteins 61, 704-721. (Pubitemid 41753142)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.61
, Issue.4
, pp. 704-721
-
-
Li, H.1
Robertson, A.D.2
Jensen, J.H.3
-
96
-
-
33846823909
-
Particle mesh Ewald: A N.log(N) method for Ewald sums in large systems
-
Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: a N.log(N) method for Ewald sums in large systems, J Chem Phys 98, 10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
97
-
-
0033468737
-
Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects
-
Srinivasan, J., Trevathan, M. W., Beroza, P., and Case, D. A. (1999) Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects, Theoretical Chemistry Accounts 101, 426-434.
-
(1999)
Theoretical Chemistry Accounts
, vol.101
, pp. 426-434
-
-
Srinivasan, J.1
Trevathan, M.W.2
Beroza, P.3
Case, D.A.4
-
98
-
-
0032905858
-
A brighter future for protein structure prediction
-
DOI 10.1038/5794
-
Koehl, P., and Levitt, M. (1999) A brighter future for protein structure prediction, Nat Struct Biol 6, 108-111. (Pubitemid 29069769)
-
(1999)
Nature Structural Biology
, vol.6
, Issue.2
, pp. 108-111
-
-
Koehl, P.1
Levitt, M.2
-
99
-
-
0036720921
-
Completion and refinement of 3-D homology models with restricted molecular dynamics: Application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis
-
DOI 10.1002/prot.10105
-
Flohil, J. A., Vriend, G., and Berendsen, H. J. (2002) Completion and refi nement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis, Proteins 48, 593-604. (Pubitemid 34925447)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.48
, Issue.4
, pp. 593-604
-
-
Flohil, J.A.1
Vriend, G.2
Berendsen, H.J.C.3
-
100
-
-
34248549547
-
Can molecular dynamics simulations provide high-resolution refinement of protein structure?
-
DOI 10.1002/prot.21345
-
Chen, J., and Brooks, C. L., 3rd. (2007) Can molecular dynamics simulations provide highresolution refi nement of protein structure?, Proteins 67, 922-930. (Pubitemid 46753939)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.67
, Issue.4
, pp. 922-930
-
-
Chen, J.1
Brooks III, C.L.2
-
101
-
-
47349128896
-
Toward better refinement of comparative models: Predicting loops in inexact environments
-
DOI 10.1002/prot.21990
-
Sellers, B. D., Zhu, K., Zhao, S., Friesner, R. A., and Jacobson, M. P. (2008) Toward better refi nement of comparative models: predicting loops in inexact environments, Proteins 72, 959-971. (Pubitemid 352000873)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.72
, Issue.3
, pp. 959-971
-
-
Sellers, B.D.1
Zhu, K.2
Zhao, S.3
Friesner, R.A.4
Jacobson, M.P.5
-
102
-
-
77955796067
-
Antibodies as a model system for comparative model refi nement
-
Sellers, B. D., Nilmeier, J. P., and Jacobson, M. P. (2010) Antibodies as a model system for comparative model refi nement, Proteins 78, 2490-2505.
-
(2010)
Proteins
, vol.78
, pp. 2490-2505
-
-
Sellers, B.D.1
Nilmeier, J.P.2
Jacobson, M.P.3
-
103
-
-
77957965659
-
Application of biasing-potential replicaexchange simulations for loop modeling and refi nement of proteins in explicit solvent
-
Kannan, S., and Zacharias, M. (2010) Application of biasing-potential replicaexchange simulations for loop modeling and refi nement of proteins in explicit solvent, Proteins 78, 2809-2819.
-
(2010)
Proteins
, vol.78
, pp. 2809-2819
-
-
Kannan, S.1
Zacharias, M.2
-
104
-
-
77955792980
-
Consistent refi nement of submitted models at CASP using a knowledge-based potential
-
Chopra, G., Kalisman, N., and Levitt, M. (2010) Consistent refi nement of submitted models at CASP using a knowledge-based potential, Proteins, 78, 2668-2678.
-
(2010)
Proteins
, vol.78
, pp. 2668-2678
-
-
Chopra, G.1
Kalisman, N.2
Levitt, M.3
-
105
-
-
33645792604
-
Physically realistic homology models built with ROSETTA can be more accurate than their templates
-
Misura, K. M., Chivian, D., Rohl, C. A., Kim, D. E., and Baker, D. (2006) Physically realistic homology models built with ROSETTA can be more accurate than their templates, Proc Natl Acad Sci U S A 103, 5361-5366.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 5361-5366
-
-
Misura, K.M.1
Chivian, D.2
Rohl, C.A.3
Kim, D.E.4
Baker, D.5
-
106
-
-
0037093644
-
Increasing the precision of comparative models with YASARA NOVA - A self-parameterizing force field
-
DOI 10.1002/prot.10104
-
Krieger, E., Koraimann, G., and Vriend, G. (2002) Increasing the precision of comparative models with YASARA NOVA-a selfparameterizing force fi eld, Proteins 47, 393-402. (Pubitemid 34438688)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.47
, Issue.3
, pp. 393-402
-
-
Krieger, E.1
Koraimann, G.2
Vriend, G.3
-
107
-
-
10344223464
-
Making optimal use of empirical energy functions: Force-field parameterization in crystal space
-
DOI 10.1002/prot.20251
-
Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A., and Vriend, G. (2004) Making optimal use of empirical energy functions: force-fi eld parameterization in crystal space, Proteins 57, 678-683. (Pubitemid 39626989)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.57
, Issue.4
, pp. 678-683
-
-
Krieger, E.1
Darden, T.2
Nabuurs, S.B.3
Finkelstein, A.4
Vriend, G.5
-
108
-
-
46149096463
-
Protein model refinement using an optimized physics-based all-atom force field
-
DOI 10.1073/pnas.0800054105
-
Jagielska, A., Wroblewska, L., and Skolnick, J. (2008) Protein model refi nement using an optimized physics-based all-atom force fi eld, Proc Natl Acad Sci U S A 105, 8268-8273. (Pubitemid 351904745)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.24
, pp. 8268-8273
-
-
Jagielska, A.1
Wroblewska, L.2
Skolnick, J.3
-
109
-
-
74249090260
-
Improving physical realismstereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8
-
Krieger, E., Joo, K., Lee, J., Raman, S., Thompson, J., Tyka, M., Baker, D., and Karplus, K. (2009) Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8, Proteins 77 Suppl 9, 114-122.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 114-122
-
-
Krieger, E.1
Joo, K.2
Lee, J.3
Raman, S.4
Thompson, J.5
Tyka, M.6
Baker, D.7
Karplus, K.8
-
110
-
-
0037571112
-
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
-
Halgren, T. A. (1996) Merck molecular force fi eld. I. Basis, form, scope, parameterization, and performance of MMFF94, J Comput Chem 17, 490-519. (Pubitemid 126567067)
-
(1996)
Journal of Computational Chemistry
, vol.17
, Issue.5-6
, pp. 490-519
-
-
Halgren, T.A.1
-
111
-
-
0011134241
-
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
-
Halgren, T. A. (1996) Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions, J Comput Chem 17, 520-552. (Pubitemid 126567068)
-
(1996)
Journal of Computational Chemistry
, vol.17
, Issue.5-6
, pp. 520-552
-
-
Halgren, T.A.1
-
112
-
-
0011143599
-
Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94
-
Halgren, T. A. (1996) Merck molecular force fi eld. III. Molecular geometries and vibrational frequencies for MMFF94, J Comput Chem 17, 553-586. (Pubitemid 126567069)
-
(1996)
Journal of Computational Chemistry
, vol.17
, Issue.5-6
, pp. 553-586
-
-
Halgren, T.A.1
-
113
-
-
0001061464
-
Merck molecular force field. IV. Conformational energies and geometries for MMFF94
-
Halgren, T. A., and Nachbar, R. B. (1996) Merck molecular force fi eld. IV. Conformational energies and geometries for MMFF94, J Comput Chem 17, 587-615. (Pubitemid 126567070)
-
(1996)
Journal of Computational Chemistry
, vol.17
, Issue.5-6
, pp. 587-615
-
-
Halgren, T.A.1
Nachbar, R.B.2
-
114
-
-
5244268272
-
Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules
-
Halgren, T. A. (1996) Merck molecular force fi eld. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules, J Comput Chem 17, 616-641. (Pubitemid 126567071)
-
(1996)
Journal of Computational Chemistry
, vol.17
, Issue.5-6
, pp. 616-641
-
-
Halgren, T.A.1
-
115
-
-
0042354622
-
Alcohols ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds
-
Allinger, N. L., Chen, K. H., Lii, J. H., and Durkin, K. A. (2003) Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force fi eld for simple compounds, J Comput Chem 24, 1447-1472.
-
(2003)
J Comput Chem
, vol.24
, pp. 1447-1472
-
-
Allinger, N.L.1
Chen, K.H.2
Lii, J.H.3
Durkin, K.A.4
-
116
-
-
0041352870
-
Alcohols ethers, carbohydrates, and related compounds. II. The anomeric effect
-
Lii, J. H., Chen, K. H., Durkin, K. A., and Allinger, N. L. (2003) Alcohols, ethers, carbohydrates, and related compounds. II. The anomeric effect, J Comput Chem 24, 1473-1489.
-
(2003)
J Comput Chem
, vol.24
, pp. 1473-1489
-
-
Lii, J.H.1
Chen, K.H.2
Durkin, K.A.3
Allinger, N.L.4
-
117
-
-
0041853579
-
Alcohols ethers, carbohydrates, and related compounds. III. The 1,2-dimethoxyethane system
-
Lii, J. H., Chen, K. H., Grindley, T. B., and Allinger, N. L. (2003) Alcohols, ethers, carbohydrates, and related compounds. III. The 1,2-dimethoxyethane system, J Comput Chem 24, 1490-1503.
-
(2003)
J Comput Chem
, vol.24
, pp. 1490-1503
-
-
Lii, J.H.1
Chen, K.H.2
Grindley, T.B.3
Allinger, N.L.4
-
118
-
-
0043062724
-
Alcohols ethers, carbohydrates, and related compounds. IV. Carbohydrates
-
Lii, J. H., Chen, K. H., and Allinger, N. L. (2003) Alcohols, ethers, carbohydrates, and related compounds. IV. Carbohydrates, J Comput Chem 24, 1504-1513.
-
(2003)
J Comput Chem
, vol.24
, pp. 1504-1513
-
-
Lii, J.H.1
Chen, K.H.2
Allinger, N.L.3
|