-
1
-
-
0034963883
-
Computational challenges in structural and functional genomics
-
Head-Gordon T, Wooley JC. Computational challenges in structural and functional genomics. IBM Systems J 2001;40:265-296.
-
(2001)
IBM Systems J
, vol.40
, pp. 265-296
-
-
Head-Gordon, T.1
Wooley, J.C.2
-
2
-
-
0035702809
-
Critical assessment of methods of protein structure prediction (CASP): Round IV
-
Moult J, Fidelis K, Zemla A, Hubbard T. Critical assessment of methods of protein structure prediction (CASP): round IV. Proteins 2001;Suppl 5:2-7.
-
(2001)
Proteins
, Issue.SUPPL. 5
, pp. 2-7
-
-
Moult, J.1
Fidelis, K.2
Zemla, A.3
Hubbard, T.4
-
3
-
-
0035782683
-
Functional inferences from blind ab initio protein structure predictions
-
Bonneau R, Tsai J, Ruczinski I, Baker D. Functional inferences from blind ab initio protein structure predictions. J Struct Biol 2001;134:186-190.
-
(2001)
J Struct Biol
, vol.134
, pp. 186-190
-
-
Bonneau, R.1
Tsai, J.2
Ruczinski, I.3
Baker, D.4
-
4
-
-
0034031680
-
Effective energy functions for protein structure prediction
-
Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000;10:139-145.
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 139-145
-
-
Lazaridis, T.1
Karplus, M.2
-
5
-
-
0032466648
-
Continuum solvent studies of the stability of RNA hairpin loops and helices
-
Srinivasan J, Miller J, Kollman PA, Case DA. Continuum solvent studies of the stability of RNA hairpin loops and helices. J Biomol Struct Dyn 1998;16:671-682.
-
(1998)
J Biomol Struct Dyn
, vol.16
, pp. 671-682
-
-
Srinivasan, J.1
Miller, J.2
Kollman, P.A.3
Case, D.A.4
-
6
-
-
0034212858
-
Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
-
Lee MR, Duan Y, Kollman PA. Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece. Proteins 2000;39:309-316.
-
(2000)
Proteins
, vol.39
, pp. 309-316
-
-
Lee, M.R.1
Duan, Y.2
Kollman, P.A.3
-
7
-
-
32844457567
-
Accurate calculation of hydration free-energies using macroscopic solvent models
-
Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free-energies using macroscopic solvent models. J Phys Chem 1994;98:1978-1988.
-
(1994)
J Phys Chem
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
8
-
-
0034788323
-
Free-energy calculations highlight differences in accuracy between x-ray and NMR structures and add value to protein structure
-
Lee MR, Kollman PA. Free-energy calculations highlight differences in accuracy between x-ray and NMR structures and add value to protein structure. Predict Struct 2001;9:905-916.
-
(2001)
Predict Struct
, vol.9
, pp. 905-916
-
-
Lee, M.R.1
Kollman, P.A.2
-
9
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley R, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990;112:6127-6129.
-
(1990)
J Am Chem Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.3
Hendrickson, T.4
-
10
-
-
0002636134
-
Pairwise descreening of solute charges from a dielectric medium
-
Hawkins G, Cramer C, Truhlar D. Pairwise descreening of solute charges from a dielectric medium. Chem Phys Lett 1995;246:122-129.
-
(1995)
Chem Phys Lett
, vol.246
, pp. 122-129
-
-
Hawkins, G.1
Cramer, C.2
Truhlar, D.3
-
11
-
-
0001246294
-
Generalized born model based on a surface integral formulation
-
Ghosh A, Rapp CS, Friesner RA. Generalized born model based on a surface integral formulation. J Phys Chem B 1998;102:10983- 10990.
-
(1998)
J Phys Chem B
, vol.102
, pp. 10983-10990
-
-
Ghosh, A.1
Rapp, C.S.2
Friesner, R.A.3
-
12
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii
-
Qiu D, Shenkin PS, Hollinger FP, Still WC. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii. J Phys Chem A 1997;101:3005-3014.
-
(1997)
J Phys Chem A
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
13
-
-
84961985307
-
Development of a generalized born model parametrization for proteins and nucleic acids
-
Dominy BN, Brooks CL III. Development of a generalized born model parametrization for proteins and nucleic acids. J Phys Chem B 1999;103:3765-3773.
-
(1999)
J Phys Chem B
, vol.103
, pp. 3765-3773
-
-
Dominy, B.N.1
Brooks C.L. III2
-
16
-
-
0012227656
-
A comprehensive analytical treatment of continuum electrostatics
-
Schaefer M, Karplus M. A comprehensive analytical treatment of continuum electrostatics J Phys Chem 1996;100:1578-1599.
-
(1996)
J Phys Chem
, vol.100
, pp. 1578-1599
-
-
Schaefer, M.1
Karplus, M.2
-
17
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
-
Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc 1998;120:9401-9409.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
18
-
-
0027080909
-
Atomic solvation parameters applied to molecular dynamics of proteins in solution
-
Wesson L, Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1992;1:227-235.
-
(1992)
Protein Sci
, vol.1
, pp. 227-235
-
-
Wesson, L.1
Eisenberg, D.2
-
19
-
-
0343128297
-
Comparative study of global minimum energy conformations of hydrated peptides
-
Klepeis JL, Floudas CA. Comparative study of global minimum energy conformations of hydrated peptides. J Comp Chem 1999;20: 636-654.
-
(1999)
J Comp Chem
, vol.20
, pp. 636-654
-
-
Klepeis, J.L.1
Floudas, C.A.2
-
20
-
-
0036138028
-
Evaluation of a fast implicit solvent model for molecular dynamics simulations
-
Ferrara P, Apostolakis J, Caflish A. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins 2002;46:24-33.
-
(2002)
Proteins
, vol.46
, pp. 24-33
-
-
Ferrara, P.1
Apostolakis, J.2
Caflish, A.3
-
21
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 1998;288:477-487.
-
(1998)
J Mol Biol
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
22
-
-
0037079585
-
Identifying native-like protein structures using physics-based potentials
-
Dominy BN, Brooks CL III. Identifying native-like protein structures using physics-based potentials. J Comp Chem 2001;23:147-160.
-
(2001)
J Comp Chem
, vol.23
, pp. 147-160
-
-
Dominy, B.N.1
Brooks C.L. III2
-
23
-
-
0032558779
-
Unfolded conformations of α-lytic protease are more stable than its native state
-
Sohl JL, Jaswal SS, Agard DA. Unfolded conformations of α-lytic protease are more stable than its native state Nature 1998;395:817-819.
-
(1998)
Nature
, vol.395
, pp. 817-819
-
-
Sohl, J.L.1
Jaswal, S.S.2
Agard, D.A.3
-
24
-
-
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;258:367-392.
-
(1996)
J Mol Biol
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
25
-
-
0032612579
-
Ab initio protein structure prediction of CASP III targets using ROSETTA
-
Simons KT, Bonneau R, Ruczinski I, Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins 1999;Suppl 3:171-176.
-
(1999)
Proteins
, Issue.SUPPL. 3
, pp. 171-176
-
-
Simons, K.T.1
Bonneau, R.2
Ruczinski, I.3
Baker, D.4
-
26
-
-
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 2000;41:40-46.
-
(2000)
Proteins
, vol.41
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
27
-
-
0034560338
-
Discrimination of near-native protein structures from misfolded models by empirical free energy functions
-
Gatchell DW, Sheldon D, Vajda S, Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins 2000;41:518-534.
-
(2000)
Proteins
, vol.41
, pp. 518-534
-
-
Gatchell, D.W.1
Sheldon, D.2
Vajda, S.3
-
28
-
-
0035882533
-
A distance-dependent atomic knowledge-based potential for improved protein structure selection
-
Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001;44:223-232.
-
(2001)
Proteins
, vol.44
, pp. 223-232
-
-
Lu, H.1
Skolnick, J.2
-
29
-
-
0035186285
-
Free energies of protein decoys provide insight into determinants of protein stability
-
Vorobjev YN, Hermans J. Free energies of protein decoys provide insight into determinants of protein stability. Protein Sci 2001;10:2498-2506.
-
(2001)
Protein Sci
, vol.10
, pp. 2498-2506
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
30
-
-
0035748353
-
Prediction targets of CASP4
-
Murzin A, Hubbard TJP. Prediction targets of CASP4. Proteins 2001;Suppl 5:8-12.
-
(2001)
Proteins
, Issue.SUPPL. 5
, pp. 8-12
-
-
Murzin, A.1
Hubbard, T.J.P.2
-
31
-
-
0035698589
-
CAFASP2: The second critical assessment of fully automated structure prediction methods
-
Fischer D, Elofsson A, Rychlewski L, Pazos F, Valencia A, Rost B, Ortiz AR, Dunbrack J, Roland L. CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins 2001;Suppl 5:171-183.
-
(2001)
Proteins
, Issue.SUPPL. 5
, pp. 171-183
-
-
Fischer, D.1
Elofsson, A.2
Rychlewski, L.3
Pazos, F.4
Valencia, A.5
Rost, B.6
Ortiz, A.R.7
Dunbrack, J.8
Roland, L.9
-
32
-
-
0034308093
-
Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models
-
Feig M, Rotkiewicz P, Kolinski A, Skolnick J, Brooks CLI. Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models. Proteins 2000;41:86-97.
-
(2000)
Proteins
, vol.41
, pp. 86-97
-
-
Feig, M.1
Rotkiewicz, P.2
Kolinski, A.3
Skolnick, J.4
Brooks, C.L.I.5
-
33
-
-
0027160197
-
Backbone-dependent Rotamer Library for Proteins: Application to side-chain prediction
-
Dunbrack RL Jr, Karplus M. Backbone-dependent Rotamer Library for Proteins: application to side-chain prediction. J Mol Biol 1993;230:543-574.
-
(1993)
J Mol Biol
, vol.230
, pp. 543-574
-
-
Dunbrack R.L., Jr.1
Karplus, M.2
-
34
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 1983;4: 187-217.
-
(1983)
J Comp 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
-
35
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott M, Dunbrack JD, Evanseck MJ, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, J.D.4
Evanseck, M.J.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, 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..
-
36
-
-
0026076664
-
Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models
-
Sharp K, Nicholls A, Friedman R, Honig B. Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. Biochemistry 1991;40:9686-9697.
-
(1991)
Biochemistry
, vol.40
, pp. 9686-9697
-
-
Sharp, K.1
Nicholls, A.2
Friedman, R.3
Honig, B.4
-
37
-
-
0020475449
-
A simple method for displaying the hydropathic character of protein
-
Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of protein J Mol Biol 1982:157:105-132
-
(1982)
J Mol Biol
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
39
-
-
0032605828
-
Processing and analysis of CASP3 protein structure predictions
-
Zemla A, Venclovas C, Moult J, Fidelis K. Processing and analysis of CASP3 protein structure predictions. Proteins 1999;Suppl 3:22-29.
-
(1999)
Proteins
, Issue.SUPPL. 3
, pp. 22-29
-
-
Zemla, A.1
Venclovas, C.2
Moult, J.3
Fidelis, K.4
-
40
-
-
0036667495
-
Modern protein force fields behave comparably in molecular dynamics simulations
-
Price DJ, Brooks CLI. Modern protein force fields behave comparably in molecular dynamics simulations. J Comp Chem 2002;23: p 1045-1057.
-
(2002)
J Comp Chem
, vol.23
, pp. 1045-1057
-
-
Price, D.J.1
Brooks, C.L.I.2
-
41
-
-
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, 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, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
42
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996;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
-
43
-
-
0023449962
-
Spin glasses and the statistical mechanics of protein folding
-
Bryngelson JD, Wolynes PG. Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 1987;84: 7524-7528.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 7524-7528
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
44
-
-
0030626588
-
The Levinthal paradox: Yesterday and today
-
Karplus M. The Levinthal paradox: yesterday and today. Fold Design 1997;2:S69-S75.
-
(1997)
Fold Design
, vol.2
-
-
Karplus, M.1
-
45
-
-
0035857402
-
2.1 and 1.8 Å average Cα RMSD structure predictions on two small proteins, HP-36 and S15
-
Lee MR, Baker D, Kollman PA. 2.1 and 1.8 Å average Cα RMSD structure predictions on two small proteins, HP-36 and S15. J Am Chem Soc 2001;123:1040-1046.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 1040-1046
-
-
Lee, M.R.1
Baker, D.2
Kollman, P.A.3
-
46
-
-
0028203492
-
Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
-
Kolinski A, Skolnick J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 1994;18:338-352.
-
(1994)
Proteins
, vol.18
, pp. 338-352
-
-
Kolinski, A.1
Skolnick, J.2
-
47
-
-
0031855094
-
Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model
-
Kolinski A, Skolnick J. Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model. Proteins 1998;32:475-494.
-
(1998)
Proteins
, vol.32
, pp. 475-494
-
-
Kolinski, A.1
Skolnick, J.2
-
48
-
-
0036283048
-
Evolution and physics in comparative protein structure modeling
-
Fiser A, Feig M, Brooks CL III, Sali A. Evolution and physics in comparative protein structure modeling. Acc Chem Res 2002;35: 413-421.
-
(2002)
Acc Chem Res
, vol.35
, pp. 413-421
-
-
Fiser, A.1
Feig, M.2
Brooks C.L. III3
Sali, A.4
|