-
1
-
-
0035703089
-
-
Bonneau,R. et al. (2001) Rosetta in CASP4: Progress in ab initio protein structure prediction. Proteins, S5, 119-126.
-
Bonneau,R. et al. (2001) Rosetta in CASP4: Progress in ab initio protein structure prediction. Proteins, S5, 119-126.
-
-
-
-
2
-
-
33745726716
-
A composite score for predicting errors in protein structure models
-
Eramian,D. et al. (2006) A composite score for predicting errors in protein structure models. Protein Sci., 15, 1653-1666.
-
(2006)
Protein Sci
, vol.15
, pp. 1653-1666
-
-
Eramian, D.1
-
3
-
-
29244479220
-
A decoy set for the thermostable subdomain from chicken villin headpiece. Comparison of different free energy estimators
-
Fogolari,F. et al. (2005) A decoy set for the thermostable subdomain from chicken villin headpiece. Comparison of different free energy estimators. BMC Bioinformatics, 6, 301.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 301
-
-
Fogolari, F.1
-
4
-
-
0347417009
-
Optimizing physical energy functions for protein folding
-
Fujitsuka,Y. et al. (2004) Optimizing physical energy functions for protein folding. Proteins, 55, 88-103.
-
(2004)
Proteins
, vol.55
, pp. 88-103
-
-
Fujitsuka, Y.1
-
5
-
-
0038386050
-
3D-Jury: A simple approach to improve protein structure prediction
-
Ginalski,K. et al. (2003) 3D-Jury: A simple approach to improve protein structure prediction. Bioinformatics, 19, 1015-1018.
-
(2003)
Bioinformatics
, vol.19
, pp. 1015-1018
-
-
Ginalski, K.1
-
6
-
-
33847361456
-
Convergence of molecular dynamics simulations of membrane proteins
-
Grossfield,A. et al. (2007) Convergence of molecular dynamics simulations of membrane proteins. Proteins, 67, 31-40.
-
(2007)
Proteins
, vol.67
, pp. 31-40
-
-
Grossfield, A.1
-
7
-
-
41349089279
-
Convergence and sampling in protein simulations
-
Hess,B. (2002) Convergence and sampling in protein simulations. Phys. Rev. E, 65, 031910.
-
(2002)
Phys. Rev. E
, vol.65
, pp. 031910
-
-
Hess, B.1
-
8
-
-
3142680776
-
Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction
-
Hsieh,M.J. and Luo,R. (2004) Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction. Proteins, 56, 475-486.
-
(2004)
Proteins
, vol.56
, pp. 475-486
-
-
Hsieh, M.J.1
Luo, R.2
-
9
-
-
10244245448
-
Developing optimal non-linear scoring function for protein design
-
Hu,C. et al. (2004) Developing optimal non-linear scoring function for protein design. Bioinformatics, 20.
-
(2004)
Bioinformatics
, vol.20
-
-
Hu, C.1
-
10
-
-
1842532008
-
A hierarchical approach to all-atom protein loop prediction
-
Jacobson,M.P. et al. (2004) A hierarchical approach to all-atom protein loop prediction. Proteins, 55, 351-367.
-
(2004)
Proteins
, vol.55
, pp. 351-367
-
-
Jacobson, M.P.1
-
11
-
-
0042921442
-
How well can we predict native contacts in proteins based on decoy structures and their energies?
-
Jiang,Z. et al. (2003) How well can we predict native contacts in proteins based on decoy structures and their energies? Proteins, 52, 598-608.
-
(2003)
Proteins
, vol.52
, pp. 598-608
-
-
Jiang, Z.1
-
12
-
-
0038708222
-
A novel approach to decoy set generation: Designing a physical energy function having local minima with native structure characteristics
-
Keasar,C. and Levitt,M. (2003) A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. J. Mol. Biol., 329, 159-174.
-
(2003)
J. Mol. Biol
, vol.329
, pp. 159-174
-
-
Keasar, C.1
Levitt, M.2
-
13
-
-
0042889108
-
Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
-
Krishnamoorthy,B. and Tropsha,A. (2003) Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics, 19, 1540-1548.
-
(2003)
Bioinformatics
, vol.19
, pp. 1540-1548
-
-
Krishnamoorthy, B.1
Tropsha, A.2
-
14
-
-
0000243829
-
Procheck: A program to check the stereochemical quality of protein structures
-
Laskowski,RA. et al. (1993) Procheck: A program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26, 283-291.
-
(1993)
J. Appl. Cryst
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
-
15
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis,T. and Karplus,M. (1999) Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol., 288, 477-487.
-
(1999)
J. Mol. Biol
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
16
-
-
2442480826
-
Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model
-
Lee,M.C. and Duan,Y. (2004) Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins, 55, 620-634.
-
(2004)
Proteins
, vol.55
, pp. 620-634
-
-
Lee, M.C.1
Duan, Y.2
-
17
-
-
65549147676
-
-
Li,X. and Liang,J. (2007) Knowledge-based energy functions for computational studies of proteins. In Xu,Y. et al. (eds), Computational Methods for Protein Structure Prediction and Modeling, 1: Basic Characterization. Biological and Medical Physics, Biomedical Engineering. Springer, New York, NY.
-
Li,X. and Liang,J. (2007) Knowledge-based energy functions for computational studies of proteins. In Xu,Y. et al. (eds), Computational Methods for Protein Structure Prediction and Modeling, Volume 1: Basic Characterization. Biological and Medical Physics, Biomedical Engineering. Springer, New York, NY.
-
-
-
-
18
-
-
28844490605
-
A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics
-
Likic,V.A. et al. (2005) A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics. Protein Sci., 14, 2955-2963.
-
(2005)
Protein Sci
, vol.14
, pp. 2955-2963
-
-
Likic, V.A.1
-
19
-
-
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
-
20
-
-
0034780030
-
Peons: A neural-network-based consensus predictor that improves fold recognition
-
Lundstrom,J. et al. (2001) Peons: A neural-network-based consensus predictor that improves fold recognition. Protein Sci., 10, 2354-2362.
-
(2001)
Protein Sci
, vol.10
, pp. 2354-2362
-
-
Lundstrom, J.1
-
21
-
-
0026610767
-
Assessment of protein models with three-dimensional profiles
-
Luthy,R. et al. (1992) Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
-
(1992)
Nature
, vol.356
, pp. 83-85
-
-
Luthy, R.1
-
22
-
-
36248954429
-
On the structural convergence of biomolecular simulations by determination of effective sample size
-
Lyman,E. and Zuckerman,D.M. (2007) On the structural convergence of biomolecular simulations by determination of effective sample size. J. Phys. Chem. B, 111, 12876-12882.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 12876-12882
-
-
Lyman, E.1
Zuckerman, D.M.2
-
23
-
-
0037452894
-
Discrimination of native protein structures using atom-atom contact scoring
-
McConkey,BJ et al. (2003) Discrimination of native protein structures using atom-atom contact scoring. Proc. Natl Acad. Sci. USA 100, 3215-3220.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 3215-3220
-
-
McConkey, B.J.1
-
24
-
-
35648988945
-
Benchmarking consensus model quality assessment for protein fold recognition
-
McGuffin,L.J. (2007) Benchmarking consensus model quality assessment for protein fold recognition. BMC Bioinformatics, 8, 345.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 345
-
-
McGuffin, L.J.1
-
25
-
-
36749042541
-
Critical assessment of methods of protein structure prediction - round VII
-
Moult,J. et al. (2007) Critical assessment of methods of protein structure prediction - round VII. Proteins, 69, 3-9.
-
(2007)
Proteins
, vol.69
, pp. 3-9
-
-
Moult, J.1
-
26
-
-
66149084059
-
Model quality assessment using distance constraints from alignments
-
Paluszewski,M. and Karplus,K. (2008) Model quality assessment using distance constraints from alignments. Proteins, 75, 540-549.
-
(2008)
Proteins
, vol.75
, pp. 540-549
-
-
Paluszewski, M.1
Karplus, K.2
-
27
-
-
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
-
28
-
-
24144437430
-
Improving sequence-based fold recognition by using 3D model quality assessment
-
Pettitt,C. et al. (2005) Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics, 21, 3509-3515.
-
(2005)
Bioinformatics
, vol.21
, pp. 3509-3515
-
-
Pettitt, C.1
-
30
-
-
0033853177
-
Decoys 'R' Us: A database of incorrect protein conformations to improve protein structure prediction
-
Samudrala,R. and Levitt,M. (2000) Decoys 'R' Us: A database of incorrect protein conformations to improve protein structure prediction. Protein Sci., 9, 1399-1401.
-
(2000)
Protein Sci
, vol.9
, pp. 1399-1401
-
-
Samudrala, R.1
Levitt, M.2
-
31
-
-
0032530578
-
Clustering of low-energy conformations near the native structures of small proteins
-
Shortle,D. et al. (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl Acad. Sci. USA, 95, 11158-11162.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 11158-11162
-
-
Shortle, D.1
-
32
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons,K. et al. (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.1
-
33
-
-
0003709653
-
Multiple Criteria Optimization, Theory, Computation, and Application
-
Wiley, New York
-
Steuer,R. (1986) Multiple Criteria Optimization, Theory, Computation, and Application. Wiley Series in Probability and Mathematical Statistics: Applied Probability and Statistics. Wiley, New York.
-
(1986)
Wiley Series in Probability and Mathematical Statistics: Applied Probability and Statistics
-
-
Steuer, R.1
-
34
-
-
0041743084
-
Predicting reliable regions in protein alignments from sequence profiles
-
Tress,M.L. et al. (2003) Predicting reliable regions in protein alignments from sequence profiles. J. Mol. Biol., 330, 705-718.
-
(2003)
J. Mol. Biol
, vol.330
, pp. 705-718
-
-
Tress, M.L.1
-
35
-
-
0038008976
-
An improved protein decoy set for testing energy functions for protein structure prediction
-
Tsai,J. et al. (2003) An improved protein decoy set for testing energy functions for protein structure prediction. Proteins, 53 76-87.
-
(2003)
Proteins
, vol.53
, pp. 76-87
-
-
Tsai, J.1
-
36
-
-
33947579390
-
Protein structure prediction by all-atom free-energy refinement
-
Verma,A. and Wenzel,W. (2007) Protein structure prediction by all-atom free-energy refinement. BMC Struct. Biol., 7, 12.
-
(2007)
BMC Struct. Biol
, vol.7
, pp. 12
-
-
Verma, A.1
Wenzel, W.2
-
37
-
-
4544355522
-
Improved protein structure selection using decoy-dependent discriminatory functions
-
Wang,K. et al. (2004) Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct. Biol., 4 8.
-
(2004)
BMC Struct. Biol
, vol.4
, pp. 8
-
-
Wang, K.1
-
38
-
-
0028895567
-
Discriminating compact nonnative structures from the native structure of globular proteins
-
Wang,Y. et al. (1995) Discriminating compact nonnative structures from the native structure of globular proteins. Proc. Natl Acad. Sci. USA, 92, 709-713.
-
(1995)
Proc. Natl Acad. Sci. USA
, vol.92
, pp. 709-713
-
-
Wang, Y.1
-
39
-
-
34547298869
-
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? - large scale AMBER benchmarking
-
Wroblewska,L. and Skolnick,J. (2007) Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? - large scale AMBER benchmarking. J. Comp. Chem., 28, 2059-2066.
-
(2007)
J. Comp. Chem
, vol.28
, pp. 2059-2066
-
-
Wroblewska, L.1
Skolnick, J.2
-
40
-
-
1842532062
-
GEMDOCK: A generic evolutionary method for molecular docking
-
Yang,J.M. and Chen,C.C. (2004) GEMDOCK: A generic evolutionary method for molecular docking. Proteins, 55, 288-304.
-
(2004)
Proteins
, vol.55
, pp. 288-304
-
-
Yang, J.M.1
Chen, C.C.2
-
41
-
-
0042622381
-
LGA: A method for finding 3D similarities in protein structure prediction
-
Zemla,A. (2003) LGA: A method for finding 3D similarities in protein structure prediction. Nucleic Acids Res., 31, 3370-3374.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
42
-
-
1642534609
-
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
-
Zhang,C. et al. (2004) An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci., 13, 400-411.
-
(2004)
Protein Sci
, vol.13
, pp. 400-411
-
-
Zhang, C.1
|