-
1
-
-
27344449197
-
Progress in modeling of protein structures and interactions
-
Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science 2005;310:638-642.
-
(2005)
Science
, vol.310
, pp. 638-642
-
-
Schueler-Furman, O.1
Wang, C.2
Bradley, P.3
Misura, K.4
Baker, D.5
-
2
-
-
33646931471
-
Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
-
Shakhnovich E. Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem Rev 2006; 106:1559-1588.
-
(2006)
Chem Rev
, vol.106
, pp. 1559-1588
-
-
Shakhnovich, E.1
-
5
-
-
30344475200
-
Progress over the first decade of CASP experiments
-
Kryshtafovych A, Venclovas C, Fidelis K, Moult J. Progress over the first decade of CASP experiments. Proteins 2005;61(S7):225-236.
-
(2005)
Proteins
, vol.61
, Issue.S7
, pp. 225-236
-
-
Kryshtafovych, A.1
Venclovas, C.2
Fidelis, K.3
Moult, J.4
-
6
-
-
12844288890
-
The protein structure prediction problem could be solved by using the current PDB library
-
Zhang Y, Skolnick J. The protein structure prediction problem could be solved by using the current PDB library. Proc Natl Acad Sci USA 2005;102:1029-1034.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 1029-1034
-
-
Zhang, Y.1
Skolnick, J.2
-
7
-
-
24944493938
-
Toward high-resolution de novo structure prediction for small proteins
-
Bradley P, Misura K, 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.2
Baker, D.3
-
8
-
-
30344447955
-
Assessment of predictions submitted for the CASP6 comparative modeling category
-
Tress M, Ezkurdia I, Grana O, Lopez G, Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins 2005;61(S7):27-45.
-
(2005)
Proteins
, vol.61
, Issue.S7
, pp. 27-45
-
-
Tress, M.1
Ezkurdia, I.2
Grana, O.3
Lopez, G.4
Valencia, A.5
-
9
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
10
-
-
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
-
11
-
-
4444351490
-
Empirical force fields for biological macromolecules: Overview and issues
-
MacKerell AD, Jr. Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 2004;25:1584-1604.
-
(2004)
J Comput Chem
, vol.25
, pp. 1584-1604
-
-
MacKerell Jr., A.D.1
-
12
-
-
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
-
13
-
-
0347994106
-
Refinement of homology-based protein structures by molecular dynamics simulation techniques
-
Fan H, Mark AE. Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci 2004;13:211-220.
-
(2004)
Protein Sci
, vol.13
, pp. 211-220
-
-
Fan, H.1
Mark, A.E.2
-
14
-
-
0032968133
-
Implicit solvent models
-
Roux B, Simonson T. Implicit solvent models. Biophys Chem 1999;78:1-20.
-
(1999)
Biophys Chem
, vol.78
, pp. 1-20
-
-
Roux, B.1
Simonson, T.2
-
15
-
-
1942456697
-
Recent advances in the development and application of implicit solvent models in biomolecule simulations
-
Feig M, Brooks CL, III. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr Opin Struct Biol 2004;14:217-224.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 217-224
-
-
Feig, M.1
Brooks III, C.L.2
-
16
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 1999;314:141-151.
-
(1999)
Chem Phys Lett
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
17
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC, 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.C.3
Hendrickson, T.4
-
18
-
-
0141956090
-
Generalized Born model with a simple smoothing function
-
Im W, Lee MS, Brooks CL, III. Generalized Born model with a simple smoothing function. J Comput Chem 2003;24:1691-1702.
-
(2003)
J Comput Chem
, vol.24
, pp. 1691-1702
-
-
Im, W.1
Lee, M.S.2
Brooks III, C.L.3
-
19
-
-
33645408056
-
Balancing solvation and intramolecular interactions: Towards a consistent generalized Born force field
-
Chen J, Im W, Brooks CL, III. Balancing solvation and intramolecular interactions: towards a consistent generalized Born force field. J Am Chem Soc 2006;128:3728-3736.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 3728-3736
-
-
Chen, J.1
Im, W.2
Brooks III, C.L.3
-
20
-
-
10344226224
-
Refinement of NMR structures using implicit solvent and advanced sampling techniques
-
Chen J, Im W, Brooks CL, III. Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc 2004;126:16038-16047.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 16038-16047
-
-
Chen, J.1
Im, W.2
Brooks III, C.L.3
-
21
-
-
20444374120
-
Generation of native-like models from limited NMR data, modern force fields and advanced conformational sampling
-
Chen J, Won H-S, Im W, Dyson HJ, Brooks CL. Generation of native-like models from limited NMR data, modern force fields and advanced conformational sampling. J Biomol NMR 2005;31: 59-64.
-
(2005)
J Biomol NMR
, vol.31
, pp. 59-64
-
-
Chen, J.1
Won, H.-S.2
Im, W.3
Dyson, H.J.4
Brooks, C.L.5
-
23
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Jr, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, 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, III, 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 Jr, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, 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..
-
24
-
-
0038054912
-
Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations
-
Feig M, MacKerell AD, Jr, Brooks CL, III. Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations. J Phys Chem 2003;107:2831-2836.
-
(2003)
J Phys Chem
, vol.107
, pp. 2831-2836
-
-
Feig, M.1
MacKerell Jr, A.D.2
Brooks III, C.L.3
-
25
-
-
1642576012
-
Improved treatment of the protein backbone in empirical force fields
-
MacKerell AD, Jr, Feig M, Brooks CL, III. Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc 2004;126:698-699.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 698-699
-
-
MacKerell Jr, A.D.1
Feig, M.2
Brooks III, C.L.3
-
27
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitation s of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
MacKerell AD, Jr, Feig M, Brooks CL, III. Extending the treatment of backbone energetics in protein force fields: limitation s of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004;25:1400-1415.
-
(2004)
J Comput Chem
, vol.25
, pp. 1400-1415
-
-
MacKerell Jr, A.D.1
Feig, M.2
Brooks III, C.L.3
-
28
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
29
-
-
0030443368
-
Protein fold recognition and dynamics in the space of contact maps
-
Mirny L, Domany E. Protein fold recognition and dynamics in the space of contact maps. Proteins 1996;26:391-410.
-
(1996)
Proteins
, vol.26
, pp. 391-410
-
-
Mirny, L.1
Domany, E.2
-
30
-
-
0032080053
-
Calculations on folding of segment B1 of streptococcal protein G
-
Sheinerman FB, Brooks CL, III. Calculations on folding of segment B1 of streptococcal protein G. J Mol Biol 1998;278:439-456.
-
(1998)
J Mol Biol
, vol.278
, pp. 439-456
-
-
Sheinerman, F.B.1
Brooks III, C.L.2
-
32
-
-
1942423619
-
MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology
-
Feig M, Karanicolas J, Brooks CL, III. MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 2004;22:377-395.
-
(2004)
J Mol Graph Model
, vol.22
, pp. 377-395
-
-
Feig, M.1
Karanicolas, J.2
Brooks III, C.L.3
-
33
-
-
84986512474
-
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
-
-
-
-
34
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland 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
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
35
-
-
0042622381
-
LGA: A method for finding 3D similarities in protein structures
-
Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003;31:3370-3374.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
37
-
-
25144472591
-
Showing your ID: Intrinsic disorder as an id for recognition, regulation and cell signaling
-
Uversky VN, Oldfieldly CJ, Dunker AK. Showing your ID: intrinsic disorder as an id for recognition, regulation and cell signaling. J Mol Recognit 2005;18:343-384.
-
(2005)
J Mol Recognit
, vol.18
, pp. 343-384
-
-
Uversky, V.N.1
Oldfieldly, C.J.2
Dunker, A.K.3
-
38
-
-
0042208326
-
On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy
-
Levy RM, Zhang LY, Gallicchio E, Felts AK. On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. J Am Chem Soc 2003;125:9523-9530.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 9523-9530
-
-
Levy, R.M.1
Zhang, L.Y.2
Gallicchio, E.3
Felts, A.K.4
|