-
1
-
-
0029018773
-
Ranking potential binding peptides to MHC molecules by a computational threading approach
-
Altuvia, Y., Schueler, O., and Margalit, H. 1995. Ranking potential binding peptides to MHC molecules by a computational threading approach. J. Mol. Biol. 249: 244-250.
-
(1995)
J. Mol. Biol.
, vol.249
, pp. 244-250
-
-
Altuvia, Y.1
Schueler, O.2
Margalit, H.3
-
2
-
-
0025146535
-
Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment. Streptomyces griseus protease A
-
Avbelj, F., Moult, J., Kitson, D.H., James, M.N., and Hagler, A.T. 1990. Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A. Biochemistry 29: 8658-8676.
-
(1990)
Biochemistry
, vol.29
, pp. 8658-8676
-
-
Avbelj, F.1
Moult, J.2
Kitson, D.H.3
James, M.N.4
Hagler, A.T.5
-
3
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4: 187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
4
-
-
0027318317
-
An empirical energy function for threading protein sequence through the folding motif
-
Bryant, S.H. and Lawrence, C.E. 1993. An empirical energy function for threading protein sequence through the folding motif. Proteins 16: 92-112.
-
(1993)
Proteins
, vol.16
, pp. 92-112
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
5
-
-
0026539511
-
Structure-derived hydrophobic potential. Hydrophobic potential derived from x-ray structures of globular proteins is able to identify native folds
-
Casari, G. and Sippl, M.J. 1992. Structure-derived hydrophobic potential. Hydrophobic potential derived from x-ray structures of globular proteins is able to identify native folds. J. Mol. Biol. 224: 725-732.
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 725-732
-
-
Casari, G.1
Sippl, M.J.2
-
6
-
-
0029844461
-
Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: Atomic burial position and pairwise non-bonded interactions
-
De Bolt, S.E. and Skolnick, J. 1996. Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: Atomic burial position and pairwise non-bonded interactions. Protein Eng. 9: 637-655.
-
(1996)
Protein Eng.
, vol.9
, pp. 637-655
-
-
De Bolt, S.E.1
Skolnick, J.2
-
7
-
-
0037079585
-
Identifying native-like protein structures using physics-based potentials
-
Dominy, B.N. and Brooks III, C.L. 2002. Identifying native-like protein structures using physics-based potentials. J. Comput. Chem. 23: 147-160.
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 147-160
-
-
Dominy, B.N.1
Brooks C.L. III2
-
8
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan, Y. and Kollman, P.A. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282: 740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
9
-
-
0036681394
-
Distinquishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized Bom solvent model
-
Felts, A.K., Gallicchio, E., Wallqvist, A., and Levy, R.M. 2002. Distinquishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized Bom solvent model. Proteins 48: 404-422.
-
(2002)
Proteins
, vol.48
, pp. 404-422
-
-
Felts, A.K.1
Gallicchio, E.2
Wallqvist, A.3
Levy, R.M.4
-
10
-
-
0028066936
-
Comparison of systematic search and database methods for constructing segments of protein structure
-
Fidelis, K., Stern, P., Bacon, D., and Moult, J. 1994. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng. 7: 953-960.
-
(1994)
Protein Eng.
, vol.7
, pp. 953-960
-
-
Fidelis, K.1
Stern, P.2
Bacon, D.3
Moult, J.4
-
12
-
-
0001246294
-
Generalized Born model based on a surface integral formulation
-
Ghosh, A., Rapp, C.S., and Friesner, R.A. 1998. Generalized Born model based on a surface integral formulation. J. Phys. Chem. B 102: 10983-10990.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 10983-10990
-
-
Ghosh, A.1
Rapp, C.S.2
Friesner, R.A.3
-
13
-
-
0029873155
-
Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials
-
Gilis, D. and Rooman, M. 1996. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J. Mol. Biol. 257: 1112-1126.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 1112-1126
-
-
Gilis, D.1
Rooman, M.2
-
14
-
-
0030777760
-
Predicting protein stability changes upon mutation using data-base-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence
-
1997. Predicting protein stability changes upon mutation using data-base-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence. J. Mol. Biol. 272: 276-290.
-
(1997)
J. Mol. Biol.
, vol.272
, pp. 276-290
-
-
-
15
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois, R., Nielsen, J.E., and Serrano, L. 2002. Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J. Mol. Biol. 302: 369-387.
-
(2002)
J. Mol. Biol.
, vol.302
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
16
-
-
0033117762
-
Designing potential energy functions for protein folding
-
Hao, M.H. and Scheraga, H.A. 1998. Designing potential energy functions for protein folding. Curr. Opin. Struct. Biol. 9: 184-188.
-
(1998)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 184-188
-
-
Hao, M.H.1
Scheraga, H.A.2
-
17
-
-
0025008445
-
Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
-
Hendlich, M., Lackner, P., Weitckus, S., Floeckner, H., Froschauer, R., Gottsbacher, K., Casari, G., and Sippl, M.J. 1990. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 216: 167-180.
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Floeckner, H.4
Froschauer, R.5
Gottsbacher, K.6
Casari, G.7
Sippl, M.J.8
-
18
-
-
0027092678
-
Selection of representive protein data sets
-
Hobohm, U., Scharf, M., Schneider, R., and Sander, C. 1992. Selection of representive protein data sets. Protein Sci. 1: 409-417.
-
(1992)
Protein Sci.
, vol.1
, pp. 409-417
-
-
Hobohm, U.1
Scharf, M.2
Schneider, R.3
Sander, C.4
-
19
-
-
0026675799
-
Fast and simple Monte Carlo algorithm for side chain optimization in proteins: Application to model building by homology
-
Holm, L. and Sander, C. 1992. Fast and simple Monte Carlo algorithm for side chain optimization in proteins: Application to model building by homology. Proteins 14: 213-223.
-
(1992)
Proteins
, vol.14
, pp. 213-223
-
-
Holm, L.1
Sander, C.2
-
20
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. A new approach to protein fold recognition. Nature 358: 86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
21
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
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.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
22
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis, T. and Karplus, M. 1998. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol. 288: 477-487.
-
(1998)
J. Mol. Biol.
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
23
-
-
0033135638
-
Effective energy function for proteins in solution
-
1999. Effective energy function for proteins in solution. Proteins 35: 133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
-
24
-
-
0034031680
-
Effective energy function for protein structure prediction
-
2000. Effective energy function for protein structure prediction. Curt. Opin. Struct. Biol. 10: 139-145.
-
(2000)
Curt. Opin. Struct. Biol.
, vol.10
, pp. 139-145
-
-
-
25
-
-
0033514939
-
Energy-based de novo protein folding by conformational space annealing and an off-lattice United-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
-
Lee, J., Liwo, A., and Scheraga, H.A. 1999. Energy-based de novo protein folding by conformational space annealing and an off-lattice United-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. Proc. Natl. Acad. Sci. 96: 2025-2030.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 2025-2030
-
-
Lee, J.1
Liwo, A.2
Scheraga, H.A.3
-
26
-
-
0000109280
-
The introduction of strain and its effects on the structure and stability of t4 lysozyme
-
Liu, R., Baase, W.A., and Mattthews, B. 2000. The introduction of strain and its effects on the structure and stability of t4 lysozyme. J. Mol. Biol. 298: 937-953.
-
(2000)
J. Mol. Biol.
, vol.298
, pp. 937-953
-
-
Liu, R.1
Baase, W.A.2
Mattthews, B.3
-
27
-
-
0035882533
-
A distance-dependent atomic knowledge-based potential for improved protein structure selection
-
Lu, H. and Skolnick, J. 2001. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 44: 223-232.
-
(2001)
Proteins
, vol.44
, pp. 223-232
-
-
Lu, H.1
Skolnick, J.2
-
28
-
-
0026610767
-
Assessment of protein models with three-dimensional profiles
-
Luthy, R., Bowie, J.U., and Eisenberg, D. 1992. Assessment of protein models with three-dimensional profiles. Nature 356: 83-85.
-
(1992)
Nature
, vol.356
, pp. 83-85
-
-
Luthy, R.1
Bowie, J.U.2
Eisenberg, D.3
-
29
-
-
0027999315
-
Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy
-
MacArthur, M.W., Laskowski, R.A., and Thornton, J.M. 1994. Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy. Curr. Opin. Struct. Biol. 4: 731-737.
-
(1994)
Curr. Opin. Struct. Biol.
, vol.4
, pp. 731-737
-
-
MacArthur, M.W.1
Laskowski, R.A.2
Thornton, J.M.3
-
30
-
-
0036145846
-
Statistical potentials for fold assessment
-
Melo, F., Sanchez, R., and Sali, A. 2002. Statistical potentials for fold assessment. Protein Sci. 430: 430-448.
-
(2002)
Protein Sci.
, vol.430
, pp. 430-448
-
-
Melo, F.1
Sanchez, R.2
Sali, A.3
-
31
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa, S., and Jernigan, R.L. 1985. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18: 534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
32
-
-
0033566614
-
An empirical energy potential with a reference state for protein fold and sequence recognition
-
Miyazawa, S. and Jernigan, R.L. 1999. An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 36: 357-369.
-
(1999)
Proteins
, vol.36
, pp. 357-369
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
33
-
-
0028864205
-
A critical assessment of comparative molecular modeling of tertiary structures of proteins
-
Mosimann, S.R.M. and James, M.N. 1995. A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 23: 301-317.
-
(1995)
Proteins
, vol.23
, pp. 301-317
-
-
Mosimann, S.R.M.1
James, M.N.2
-
34
-
-
0030914617
-
Comparison of database potentials and molecular mechanics force fields
-
Moult, J. 1997. Comparison of database potentials and molecular mechanics force fields. Curr. Opin. Struct. Biol. 7: 194-199.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 194-199
-
-
Moult, J.1
-
35
-
-
0022788691
-
An algorithm for determining the conformation of polypeptide segments in proteins by systmatic search
-
Moult, J. and James, M.N.G. 1986. An algorithm for determining the conformation of polypeptide segments in proteins by systmatic search. Proteins 2: 146-163.
-
(1986)
Proteins
, vol.2
, pp. 146-163
-
-
Moult, J.1
James, M.N.G.2
-
36
-
-
0000036869
-
Simulation of activation free energies in molecular systems
-
Neria, E., Fischer, S., and Karplus, M. 1996. Simulation of activation free energies in molecular systems. J. Chem. Phys. 105: 1902-1921.
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
37
-
-
0029987862
-
Energy functions that discriminate x-ray and near native folds from well-constructed decoys
-
Park, B. and Levitt, M. 1996. Energy functions that discriminate x-ray and near native folds from well-constructed decoys. J. Mol. Biol. 258: 367-392.
-
(1996)
J. Mol. Biol.
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
38
-
-
0031556019
-
Protein folding simulations with genetic algorithms and a detailed molecular description
-
Pedersen, J.T. and Moult, J. 1997. Protein folding simulations with genetic algorithms and a detailed molecular description. J. Mol. Biol. 269: 240-259.
-
(1997)
J. Mol. Biol.
, vol.269
, pp. 240-259
-
-
Pedersen, J.T.1
Moult, J.2
-
39
-
-
0027516008
-
Computer simulation of antibody binding specificity
-
Pellegrini, M. and Doniach, S. 1993. Computer simulation of antibody binding specificity. Proteins 15: 436-444.
-
(1993)
Proteins
, vol.15
, pp. 436-444
-
-
Pellegrini, M.1
Doniach, S.2
-
40
-
-
0034486196
-
Free energy determinants of tertiary structure and the evaluation of protein models
-
Petrey, D. and Honig, B. 2000. Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci. 9: 2181-2191.
-
(2000)
Protein Sci.
, vol.9
, pp. 2181-2191
-
-
Petrey, D.1
Honig, B.2
-
41
-
-
0035956886
-
Recent improvements in prediction of protein structure by global optimization of a potential energy function
-
Pillardy, J., Czaplewski, C., Liwo, A., Lee, J., Ripoll, D.R., Kamierkiewicz, R., Oldziej, S., Wedemeyer, W.J., Gibson, K.D., Arnautova, Y.A., Saunders, J., Ye, Y.-J., and Scheraga, H.A. 2001. Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc. Natl. Acad. Sci. 98: 2329-2333.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 2329-2333
-
-
Pillardy, J.1
Czaplewski, C.2
Liwo, A.3
Lee, J.4
Ripoll, D.R.5
Kamierkiewicz, R.6
Oldziej, S.7
Wedemeyer, W.J.8
Gibson, K.D.9
Arnautova, Y.A.10
Saunders, J.11
Ye, Y.-J.12
Scheraga, H.A.13
-
42
-
-
0033168866
-
Knowledge-based interaction potentials for proteins
-
Rojnuckarin, A. and Subramaniam, S. 1999. Knowledge-based interaction potentials for proteins. Proteins 36: 54-67.
-
(1999)
Proteins
, vol.36
, pp. 54-67
-
-
Rojnuckarin, A.1
Subramaniam, S.2
-
43
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala, R. and Moult, J. 1998. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J. Mol. Biol. 275: 895-916.
-
(1998)
J. Mol. Biol.
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
44
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott, W.R.P., Hunenberger, P.H., Tironi, I.G., Mark, A.E., Billeter. S.R., Fennen, J., Torda, A.E., Huber, T., Kruger, P., and van Gunsteren, W.F. 1999. The GROMOS biomolecular simulation program package. J. Phys. Chem. A 103: 3596-3607.
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hunenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Kruger, P.9
Van Gunsteren, W.F.10
-
45
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
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.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
46
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl, M.J. 1990. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213: 859-883.
-
(1990)
J. Mol. Biol.
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
47
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
Sippl, M.J. 1993. Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355-362.
-
(1993)
Proteins
, vol.17
, pp. 355-362
-
-
Sippl, M.J.1
-
48
-
-
0031575423
-
M ONSSTER: A method for folding globular proteins with a small number of distance restraints
-
Skolnick, J., Kolinski, A., and Ortiz, A.R. 1997. M ONSSTER: A method for folding globular proteins with a small number of distance restraints. J. Mol. Biol. 265: 217-241.
-
(1997)
J. Mol. Biol.
, vol.265
, pp. 217-241
-
-
Skolnick, J.1
Kolinski, A.2
Ortiz, A.R.3
-
49
-
-
0033970623
-
Derivation of protein-specific pair potentials based on weak sequence fragment similarity
-
2000. Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins 38: 3-16.
-
(2000)
Proteins
, vol.38
, pp. 3-16
-
-
-
50
-
-
0027503403
-
Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms
-
Sun, S. 1993. Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms. Protein Sci. 2: 762-785.
-
(1993)
Protein Sci.
, vol.2
, pp. 762-785
-
-
Sun, S.1
-
51
-
-
0026503169
-
Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography
-
Svensson, L.A., Thulin, E., and Forsen, S. 1992. Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography. J. Mol. Biol. 223: 601-606.
-
(1992)
J. Mol. Biol.
, vol.223
, pp. 601-606
-
-
Svensson, L.A.1
Thulin, E.2
Forsen, S.3
-
52
-
-
0017021957
-
Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
-
Tanaka, S. and Scheraga, H.A. 1976. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 9: 945-950.
-
(1976)
Macromolecules
, vol.9
, pp. 945-950
-
-
Tanaka, S.1
Scheraga, H.A.2
-
53
-
-
0029976427
-
Statistical potentials extracted from protein structures: How accurate are they?
-
Thomas, P.D. and Dill, K.A. 1996. Statistical potentials extracted from protein structures: How accurate are they? J. Mol. Biol. 257: 457-469.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 457-469
-
-
Thomas, P.D.1
Dill, K.A.2
-
54
-
-
0034308163
-
Distance-dependent, pair potential for protein folding: Results from linear optimization
-
Tobi, D. and Elber, R. 2000. Distance-dependent, pair potential for protein folding: Results from linear optimization. Proteins 41: 40-46.
-
(2000)
Proteins
, vol.41
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
55
-
-
0034332976
-
Comparison of two optimization methods to derive energy parameters for protein folding: Perceptron and Z score
-
Vendruscolo, M., Mirny, L.A., Shakhnovich, E.I., and Domany, E. 2000. Comparison of two optimization methods to derive energy parameters for protein folding: Perceptron and Z score. Proteins 41: 192-201.
-
(2000)
Proteins
, vol.41
, pp. 192-201
-
-
Vendruscolo, M.1
Mirny, L.A.2
Shakhnovich, E.I.3
Domany, E.4
-
56
-
-
0029119320
-
A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
-
Wallqvist, A., Jernigan, R.L., and Covell, D.G. 1995. A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design. Protein Sci. 4: 1881-1903.
-
(1995)
Protein Sci.
, vol.4
, pp. 1881-1903
-
-
Wallqvist, A.1
Jernigan, R.L.2
Covell, D.G.3
-
57
-
-
1442322419
-
Detecting native protein folds among large decoy sets with the OPLS all-atom potential and the surface generalized Born solvent model
-
Wallqvist, A., Gallicchio, E., Felts, A.K., and Levy, R.M. 2002. Detecting native protein folds among large decoy sets with the OPLS all-atom potential and the surface generalized Born solvent model. Adv. Chem. Phys. 120: 459-486.
-
(2002)
Adv. Chem. Phys.
, vol.120
, pp. 459-486
-
-
Wallqvist, A.1
Gallicchio, E.2
Felts, A.K.3
Levy, R.M.4
-
58
-
-
84988053694
-
An all atom force field for simulations of proteins and nucleic acids
-
Weiner, S.J., Kollman, P., Nguyen, D., and Case, D. 1986. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7: 230-252.
-
(1986)
J. Comput. Chem.
, vol.7
, pp. 230-252
-
-
Weiner, S.J.1
Kollman, P.2
Nguyen, D.3
Case, D.4
-
59
-
-
0034733381
-
Ab initio construction of protein tertiary structures using a hierarchical approach
-
Xia, Y., Huang, E.S., Levitt, M., and Samudrala, R. 2000. Ab initio construction of protein tertiary structures using a hierarchical approach. J. Mol. Biol. 300: 171-185.
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 171-185
-
-
Xia, Y.1
Huang, E.S.2
Levitt, M.3
Samudrala, R.4
-
60
-
-
0031552370
-
Determination of atomic desolvation energies from the structures of crystallized proteins
-
Zhang, C., Vasmatzis, G., Cornette, J., and De Lisi, C. 1997. Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol. 267: 707-726.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 707-726
-
-
Zhang, C.1
Vasmatzis, G.2
Cornette, J.3
De Lisi, C.4
-
61
-
-
20644436466
-
Solvent models for protein-ligand binding: Comparison of implicit solvent Poisson and surface generalized Born models with explicit solvent simulations
-
Zhang, L.Y., Gallicchio, E., Friesner, R.A., and Levy, R.M. 2001. Solvent models for protein-ligand binding: Comparison of implicit solvent Poisson and surface generalized Born models with explicit solvent simulations. J. Comput. Chem. 22: 591-607.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 591-607
-
-
Zhang, L.Y.1
Gallicchio, E.2
Friesner, R.A.3
Levy, R.M.4
|