-
1
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181.
-
(1973)
Science
, vol.181
-
-
Anfinsen, C.B.1
-
2
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Jr, Bashford D, Bellott M, Dunbrack RL, Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Mich-Nick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, 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
Mich-Nick, 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
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
3
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;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 Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
4
-
-
5944250450
-
Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
-
Momany FA, McGuire RF, Burgess AW, Scheraga HA. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J Phys Chem 1975;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
-
5
-
-
0001731773
-
Energy parameters in polypeptides. X. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
-
Némethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA. Energy parameters in polypeptides. X. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 1992;96:6472-6484.
-
(1992)
J Phys Chem
, vol.96
, pp. 6472-6484
-
-
Némethy, 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
-
6
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott WRP, Hunenberger PH, Trioni IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, VanGunsteren WF. The GROMOS biomolecular simulation program package. J Phys Chem A 1997;103:3596-3607.
-
(1997)
J Phys Chem A
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hunenberger, P.H.2
Trioni, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Kruger, P.9
Vangunsteren, W.F.10
-
8
-
-
0028895567
-
Discriminating compact non-native structures from the native structures of globular proteins
-
Wang Y, Zhang H, Li W, Scott RA. Discriminating compact non-native structures from the native structures of globular proteins. Proc Natl Acad Sci USA 1995;92:709-713.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 709-713
-
-
Wang, Y.1
Zhang, H.2
Li, W.3
Scott, R.A.4
-
9
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Giffiland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Giffiland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
10
-
-
0017021957
-
Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
-
Tanaka S, Scheraga HA. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 1976;9:945-950.
-
(1976)
Macromolecules
, vol.9
, pp. 945-950
-
-
Tanaka, S.1
Scheraga, H.A.2
-
12
-
-
0026016378
-
The frequency of ion-pair substructures in proteins is quantitaively related to electrostatic potential: A statistical model for nonbonded interactions
-
Bryant SH, Lawrence CE. The frequency of ion-pair substructures in proteins is quantitaively related to electrostatic potential: a statistical model for nonbonded interactions. Proteins: Struct Funct Bioinformatics 1991;9:108-119.
-
(1991)
Proteins: Struct Funct Bioinformatics
, vol.9
, pp. 108-119
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
13
-
-
0029942661
-
Structure-derived potentials and protein simulations
-
Jernigan RL, Bahar I. Structure-derived potentials and protein simulations. Curr Opin Struct Biol 1996;6:195-209.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 195-209
-
-
Jernigan, R.L.1
Bahar, I.2
-
14
-
-
0000095892
-
A united-residue force field for off-lattice protein structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data
-
Liwo A, Oldziej S, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. A united-residue force field for off-lattice protein structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. J Comput Chem 1997;18:849-873.
-
(1997)
J Comput Chem
, vol.18
, pp. 849-873
-
-
Liwo, A.1
Oldziej, S.2
Pincus, M.R.3
Wawak, R.J.4
Rackovsky, S.5
Scheraga, H.A.6
-
15
-
-
0000095890
-
A united-residue force field for off-lattice protein structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by z-score optimization
-
Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Oldziej S, Scheraga HA. A united-residue force field for off-lattice protein structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by z-score optimization. J Comput Chem 1997;18:874-887.
-
(1997)
J Comput Chem
, vol.18
, pp. 874-887
-
-
Liwo, A.1
Pincus, M.R.2
Wawak, R.J.3
Rackovsky, S.4
Oldziej, S.5
Scheraga, H.A.6
-
16
-
-
0001181898
-
A united-residue force field for off-lattice protein structure simulations. III. Origin of backbone hydrogen bonding cooperativity in united residue potential
-
Liwo A, Kazmierkiewicz R, Czaplewski C, Groth M, Oldziej S, Wawak RJ, Rackovsky S, Pincus MR, Scheraga HA. A united-residue force field for off-lattice protein structure simulations. III. Origin of backbone hydrogen bonding cooperativity in united residue potential J Comput Chem 1998;19:259-276.
-
(1998)
J Comput Chem
, vol.19
, pp. 259-276
-
-
Liwo, A.1
Kazmierkiewicz, R.2
Czaplewski, C.3
Groth, M.4
Oldziej, S.5
Wawak, R.J.6
Rackovsky, S.7
Pincus, M.R.8
Scheraga, H.A.9
-
17
-
-
3142681595
-
Parametrization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems
-
Liwo A, Odziej S, Czaplewski C, Kozlowska U, Scheraga HA. Parametrization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems. J Phys Chem B 2004;108:9421-9438.
-
(2004)
J Phys Chem B
, vol.108
, pp. 9421-9438
-
-
Liwo, A.1
Odziej, S.2
Czaplewski, C.3
Kozlowska, U.4
Scheraga, H.A.5
-
18
-
-
0035882533
-
A distance-dependent knowledge-based potential for improved protein structure selection
-
Lu H, Skolnick J. A distance-dependent knowledge-based potential for improved protein structure selection. Proteins: Struct Funct Bioinformatics 2001;44:223-232.
-
(2001)
Proteins: Struct Funct Bioinformatics
, vol.44
, pp. 223-232
-
-
Lu, H.1
Skolnick, J.2
-
19
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998;275:895-916.
-
(1998)
J Mol Biol
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
20
-
-
0030341420
-
A knowledge-based method for protein structure refinement and prediction
-
States D, Agarwal P, Gaasterland T, Hunter L, Smith R, editors. Boston, MA: AAAI Press
-
Subramaniam S, Tcheng DK, Fenton J. A knowledge-based method for protein structure refinement and prediction. In: States D, Agarwal P, Gaasterland T, Hunter L, Smith R, editors. Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology. Boston, MA: AAAI Press; 1996. pp 218-229.
-
(1996)
Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology
, pp. 218-229
-
-
Subramaniam, S.1
Tcheng, D.K.2
Fenton, J.3
-
21
-
-
0029844461
-
Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of proteins structures: Atomic burial position and pairwise non-bonded interactions
-
DeBolt S, Skolnick J. Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of proteins structures: atomic burial position and pairwise non-bonded interactions. Protein Eng 1996;9:637-655.
-
(1996)
Protein Eng
, vol.9
, pp. 637-655
-
-
DeBolt, S.1
Skolnick, J.2
-
22
-
-
0346458791
-
A new pairwise folding potential based on improved decoy generation and side-chain packing
-
Loose C, Klepeis JL, Floudas CA. A new pairwise folding potential based on improved decoy generation and side-chain packing. Proteins: Struct Funct Bioinformatics 2004;54:303-314.
-
(2004)
Proteins: Struct Funct Bioinformatics
, vol.54
, pp. 303-314
-
-
Loose, C.1
Klepeis, J.L.2
Floudas, C.A.3
-
23
-
-
0034308163
-
Distance-dependent, pair potential for protein folding: Results from linear optimization
-
Tobi D, Elber R. Distance-dependent, pair potential for protein folding: results from linear optimization. Proteins: Struct Funct Bioinformatics 2000;41:40-46.
-
(2000)
Proteins: Struct Funct Bioinformatics
, vol.41
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
24
-
-
0028149160
-
Exploring conformational space with a simple lattice model for protein structure
-
Hinds DA, Levitt M. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 1994;243:668-682.
-
(1994)
J Mol Biol
, vol.243
, pp. 668-682
-
-
Hinds, D.A.1
Levitt, M.2
-
25
-
-
27844505722
-
Advances in protein structure prediction and de novo protein design: A review
-
Floudas CA, Fung HK, McAllister SR, Mönnigmann M, Rajgaria R. Advances in protein structure prediction and de novo protein design: a review. Chem Eng Sci 2006;61:966-988.
-
(2006)
Chem Eng Sci
, vol.61
, pp. 966-988
-
-
Floudas, C.A.1
Fung, H.K.2
McAllister, S.R.3
Mönnigmann, M.4
Rajgaria, R.5
-
27
-
-
4344598766
-
Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction
-
Misura KMS, Morozov AV, Baker D. Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. J Mol Biol 2004;342:651-664.
-
(2004)
J Mol Biol
, vol.342
, pp. 651-664
-
-
Misura, K.M.S.1
Morozov, A.V.2
Baker, D.3
-
28
-
-
24944493938
-
Toward high-resolution de novo structure prediction for small proteins
-
Bradley P, Misura KMS, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 2005;309:1868-1871.
-
(2005)
Science
, vol.309
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.S.2
Baker, D.3
-
30
-
-
0031566950
-
Inter-residue potential in globular proteins and the dominance of highly specific hydrophillic interactions at close separation
-
Bahar I, Jernigan RL. Inter-residue potential in globular proteins and the dominance of highly specific hydrophillic interactions at close separation. J Mol Biol 1997;266:195-214.
-
(1997)
J Mol Biol
, vol.266
, pp. 195-214
-
-
Bahar, I.1
Jernigan, R.L.2
-
33
-
-
2442676589
-
Automated structure prediction of weakly homologous proteins on a genomic scale
-
Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004;101:7594-7599.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 7594-7599
-
-
Zhang, Y.1
Skolnick, J.2
-
34
-
-
0031576336
-
Torsion angle dynamics for NMR structure calculation with the new program DYANA
-
Güntert P, Mumenthaler C, Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997;273:283-298.
-
(1997)
J Mol Biol
, vol.273
, pp. 283-298
-
-
Güntert, P.1
Mumenthaler, C.2
Wüthrich, K.3
-
35
-
-
0037079580
-
Maximum feasibility guideline in the design and analysis of protein folding potentials
-
Meller J, Wagner M, Elber R. Maximum feasibility guideline in the design and analysis of protein folding potentials. J Comput Chem 2002;23:111-118.
-
(2002)
J Comput Chem
, vol.23
, pp. 111-118
-
-
Meller, J.1
Wagner, M.2
Elber, R.3
-
36
-
-
0029987862
-
Energy functions that discriminate X-ray and near native folds from well-constructed decoys
-
Park B, Levitt M. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 1996; 258:367.
-
(1996)
J Mol Biol
, vol.258
, pp. 367
-
-
Park, B.1
Levitt, M.2
-
37
-
-
0346458791
-
A new pairwise folding potential based on improved decoy generation and side-chain packing
-
Loose C, Klepeis JL, Floudas CA. A new pairwise folding potential based on improved decoy generation and side-chain packing. Proteins: Struct Funct Bioinformatics 2004;54:303-314.
-
(2004)
Proteins: Struct Funct Bioinformatics
, vol.54
, pp. 303-314
-
-
Loose, C.1
Klepeis, J.L.2
Floudas, C.A.3
|