-
1
-
-
0034060287
-
Structural genomics and its importance for gene function analysis
-
DOI 10.1038/73723
-
J. Skolnick, J. S. Fetrow, and A. Kolinski, Structural genomics and its importance for gene function analysis, Nat. Biotechnol., vol. 18, pp. 283-287, 2000. (Pubitemid 30159478)
-
(2000)
Nature Biotechnology
, vol.18
, Issue.3
, pp. 283-287
-
-
Skolnick, J.1
Fetrow, J.S.2
Kolinski, A.3
-
2
-
-
0035812694
-
Protein structure prediction and structural genomics
-
DOI 10.1126/science.1065659
-
D. Baker, Protein structure prediction and structural genomics, Science, vol. 294, pp. 93-96, 2001. (Pubitemid 32952955)
-
(2001)
Science
, vol.294
, Issue.5540
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
3
-
-
12844260161
-
Comparative protein structure modeling and its applications to drug discovery
-
J. Overington, Ed. London, UK: Inpharmatica Ltd.
-
M. Jacobson and A. Sali, Comparative protein structure modeling and its applications to drug discovery, in Annual Reports in Medicinal Chemistry, J. Overington, Ed. London, UK: Inpharmatica Ltd., 2004, vol. 39, pp. 259-276.
-
(2004)
Annual Reports in Medicinal Chemistry
, vol.39
, pp. 259-276
-
-
Jacobson, M.1
Sali, A.2
-
4
-
-
17144425763
-
Practical lessons from protein structure prediction
-
DOI 10.1093/nar/gki327
-
K. Ginalski, N. V. Grishin, A. Godzik, and L. Rychlewski, Practical lessons from protein structure prediction, Nucleic Acids Res., vol. 33, pp. 1874-1891, 2005. (Pubitemid 41748333)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.6
, pp. 1874-1891
-
-
Ginalski, K.1
Grishin, N.V.2
Godzik, A.3
Rychlewski, L.4
-
5
-
-
66149123302
-
Protein structure prediction by pro-Sp3-TASSER
-
H. Zhou and J. Skolnick, Protein structure prediction by pro-Sp3-TASSER, Biophys J., vol. 96, pp. 2119-2127, 2009.
-
(2009)
Biophys J.
, vol.96
, pp. 2119-2127
-
-
Zhou, H.1
Skolnick, J.2
-
6
-
-
34347375915
-
The protein folding problem: When will it be solved?
-
DOI 10.1016/j.sbi.2007.06.001, PII S0959440X07000772, Nucleic acids / Sequences and topology
-
K. A. Dill, S. B. Ozkan, T. R. Weikl, J. D. Chodera, and V. A. Voelz, The protein folding problem: When will it be solved? Curr. Opin. Struct. Biol., vol. 17, pp. 342-346, 2007. (Pubitemid 47021366)
-
(2007)
Current Opinion in Structural Biology
, vol.17
, Issue.3
, pp. 342-346
-
-
Dill, K.A.1
Ozkan, S.B.2
Weikl, T.R.3
Chodera, J.D.4
Voelz, V.A.5
-
7
-
-
77954065271
-
I-TASSER: A unified platform for automated protein structure and function prediction
-
A. Roy, A. Kucukural, and Y. Zhang, I-TASSER: A unified platform for automated protein structure and function prediction, Nat. Protoc., vol. 5, pp. 725-738, 2010.
-
(2010)
Nat. Protoc.
, vol.5
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
8
-
-
29144526714
-
Protein structure prediction: Inroads to biology
-
DOI 10.1016/j.molcel.2005.12.005, PII S1097276505018472
-
D. Petrey and B. Honig, Protein structure prediction: Inroads to biology, Mol. Cell, vol. 20, pp. 811-819, 2005. (Pubitemid 41814871)
-
(2005)
Molecular Cell
, vol.20
, Issue.6
, pp. 811-819
-
-
Petrey, D.1
Honig, B.2
-
9
-
-
50649095790
-
Macromolecular modeling with rosetta
-
R. Das and D. Bake, Macromolecular modeling with rosetta, Annu. Rev. Biochem., vol. 77, pp. 363-382, 2008.
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 363-382
-
-
Das, R.1
Bake, D.2
-
10
-
-
64549115839
-
Protein structure prediction: When is it useful?
-
Y. Zhang, Protein structure prediction: When is it useful? Curr. Opin. Struct. Biol., vol. 19, pp. 145-155, 2009.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 145-155
-
-
Zhang, Y.1
-
11
-
-
44949145113
-
Progress and challenges in protein structure prediction
-
Y. Zhang, Progress and challenges in protein structure prediction, Curr. Opin. Struct. Biol., vol. 18, pp. 342-348, 2008.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 342-348
-
-
Zhang, Y.1
-
12
-
-
0033954256
-
The Protein Data Bank
-
H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H.Weissig, I. N. Shindyalov, and P. E. Bourne, The protein data bank, Nucleic Acids Res., vol. 28, pp. 235-242, 2000. (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, 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
-
13
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
DOI 10.1146/annurev.biophys.29.1.291
-
M. A. Martí-Renom, A. C. Stuart, A. Fiser, R. Sánchez, F. Melo, and A. Sali, Comparative protein structure modeling of genes and genomes, Annu. Rev. Biophys. Biomol. Struct., vol. 29, pp. 291-325, 2000. (Pubitemid 30599596)
-
(2000)
Annual Review of Biophysics and Biomolecular Structure
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
14
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
DOI 10.1006/jmbi.1997.0959
-
K. T. Simons, C. Kooperberg, E. Huang, and D. Baker, Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions, J. Mol. Biol., vol. 268, pp. 209-225, 1997. (Pubitemid 27192690)
-
(1997)
Journal of Molecular Biology
, vol.268
, Issue.1
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
15
-
-
30344488120
-
TASSER: An automated method for the prediction of protein tertiary structures in CASP6
-
DOI 10.1002/prot.20724
-
Y. Zhang, A. K. Arakaki, and J. Skolnick, TASSER: An automated method for the prediction of protein tertiary structures in CASP6, Proteins, vol. 61(S7), pp. 91-98, 2005. (Pubitemid 43069961)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.61
, Issue.SUPPL. 7
, pp. 91-98
-
-
Zhang, Y.1
Arakaki, A.K.2
Skolnick, J.3
-
16
-
-
0034733381
-
Ab initio construction of protein tertiary structures using a hierarchical approach
-
Y. Xia, E. S. Huang, M. Levitt, and R. Samudrala, Ab initio construction of protein tertiary structures using a hierarchical approach, J. Mol. Biol., vol. 300, pp. 171-185, 2000.
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 171-185
-
-
Xia, Y.1
Huang, E.S.2
Levitt, M.3
Samudrala, R.4
-
17
-
-
60849124513
-
Generalized ensemble methods for de novo structure prediction
-
A. Shmygelska and M. Levitt, Generalized ensemble methods for de novo structure prediction, Proc. Natl. Acad. Sci. USA, vol. 106, pp. 1415-1420, 2009.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 1415-1420
-
-
Shmygelska, A.1
Levitt, M.2
-
18
-
-
42449122271
-
Ranking predicted protein structures with support vector regression
-
DOI 10.1002/prot.21809
-
J. Qiu, W. Sheffler, D. Baker, and W. S. Noble, Ranking predicted protein structures with support vector regression, Proteins, vol. 71, pp. 1175-1182, 2008. (Pubitemid 351564044)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.71
, Issue.3
, pp. 1175-1182
-
-
Qiu, J.1
Sheffler, W.2
Baker, D.3
Noble, W.S.4
-
19
-
-
70349241497
-
Sampling bottlenecks in de novo protein structure prediction
-
D. E. Kim, B. Blum, P. Bradley, and D. Baker, Sampling bottlenecks in de novo protein structure prediction, J. Mol. Biol., vol. 393, pp. 249-260, 2009.
-
(2009)
J. Mol. Biol.
, vol.393
, pp. 249-260
-
-
Kim, D.E.1
Blum, B.2
Bradley, P.3
Baker, D.4
-
20
-
-
14644438345
-
Progress and challenges in high-resolution refinement of protein structure models
-
DOI 10.1002/prot.20376
-
K. M. Misura and D. Baker, Progress and challenges in high-resolution refinement of protein structure models, Proteins, vol. 59, pp. 15-29, 2005. (Pubitemid 40316474)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.1
, pp. 15-29
-
-
Misura, K.M.S.1
Baker, D.2
-
21
-
-
34547298869
-
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking
-
DOI 10.1002/jcc.20720
-
L. Wroblewska and J. Skolnick, Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking, J. Comput. Chem., vol. 28, pp. 2059-2066, 2007. (Pubitemid 47153603)
-
(2007)
Journal of Computational Chemistry
, vol.28
, Issue.12
, pp. 2059-2066
-
-
Wroblewska, L.1
Skolnick, J.2
-
22
-
-
46149096463
-
Protein model refinement using an optimized physics-based all-atom force field
-
DOI 10.1073/pnas.0800054105
-
A. Jagielska, L. Wroblewska, and J. Skolnick, Protein model refinement using an optimized physics-based allatom force field, Proc. Natl. Acad. Sci. USA, vol. 105, pp. 8268-8273, 2008. (Pubitemid 351904745)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.24
, pp. 8268-8273
-
-
Jagielska, A.1
Wroblewska, L.2
Skolnick, J.3
-
23
-
-
84878553777
-
Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
-
J. Skolnick, H. Zhou, and M. Gao, Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Curr. Opin. Struct. Biol., vol. 23, pp. 191-197, 2013.
-
(2013)
Curr. Opin. Struct. Biol.
, vol.23
, pp. 191-197
-
-
Skolnick, J.1
Zhou, H.2
Gao, M.3
-
24
-
-
36449000646
-
Transition states and folding dynamics of proteins and heteropolymers
-
H. S. Chan and K. A. Dill, Transition states and folding dynamics of proteins and heteropolymers, J. Chem. Phys., vol. 100, pp. 9238-9257, 1994.
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9238-9257
-
-
Chan, H.S.1
Dill, K.A.2
-
25
-
-
0030628825
-
Theory of Protein Folding: The Energy Landscape Perspective
-
J. N. Onuchic, Z. Luthey-Schulten, and P. G. Wolynes, Theory of protein folding: The energy landscape perspective, Annu. Rev. Phys. Chem., vol. 48, pp. 545-600, 1997. (Pubitemid 127443918)
-
(1997)
Annual Review of Physical Chemistry
, vol.48
, Issue.1
, pp. 545-600
-
-
Onuchic, J.N.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
26
-
-
48249134448
-
The protein folding problem
-
K. A. Dill, S. B. Ozkan, M. S. Shell, and T. R. Weikl, The protein folding problem, Annu. Rev. Bipohys., vol. 37, pp. 289-316, 2008.
-
(2008)
Annu. Rev. Bipohys.
, vol.37
, pp. 289-316
-
-
Dill, K.A.1
Ozkan, S.B.2
Shell, M.S.3
Weikl, T.R.4
-
27
-
-
33750555073
-
An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials
-
S.-Y. Huang and X. Zou, An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials, J. Comput. Chem., vol. 27, pp. 1865-1875, 2006.
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 1865-1875
-
-
Huang, S.-Y.1
Zou, X.2
-
28
-
-
33750574927
-
An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function
-
DOI 10.1002/jcc.20505
-
S.-Y. Huang and X. Zou, An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function, J. Comput. Chem., vol. 27, pp. 1876-1882, 2006. (Pubitemid 44672569)
-
(2006)
Journal of Computational Chemistry
, vol.27
, Issue.15
, pp. 1876-1882
-
-
Huang, S.-Y.1
Zou, X.2
-
29
-
-
46449084711
-
An iterative knowledge-based scoring function for protein-protein recognition
-
DOI 10.1002/prot.21949
-
S.-Y. Huang and X. Zou, An iterative knowledge-based scoring function for protein-protein recognition, Proteins, vol. 72, pp. 557-579, 2008. (Pubitemid 351928512)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.72
, Issue.2
, pp. 557-579
-
-
Huang, S.-Y.1
Zou, X.2
-
30
-
-
80051564821
-
Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures
-
S.-Y. Huang and X. Zou, Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures, Proteins, vol. 79, pp. 2648-2661, 2011.
-
(2011)
Proteins
, vol.79
, pp. 2648-2661
-
-
Huang, S.-Y.1
Zou, X.2
-
31
-
-
2442676589
-
Automated structure prediction of weakly homologous proteins on a genomic scale
-
DOI 10.1073/pnas.0305695101
-
Y. Zhang and J. Skolnick, Automated structure prediction of weakly homologous proteins on a genomic scale, Proc. Natl. Acad. Sci. USA, vol. 101, pp. 7594-7599, 2004. (Pubitemid 38658074)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.20
, pp. 7594-7599
-
-
Zhang, Y.1
Skolnick, J.2
-
32
-
-
0031576336
-
Torsion angle dynamics for NMR structure calculation with the new program DYANA
-
DOI 10.1006/jmbi.1997.1284
-
P. Guntert, C. Mumenthaler, and K. Wuthrich, Torsion angle dynamics for NMR structure calculation with the new program DYANA, J. Mol. Biol., vol. 273, pp. 283-298, 1997. (Pubitemid 27460230)
-
(1997)
Journal of Molecular Biology
, vol.273
, Issue.1
, pp. 283-298
-
-
Guntert, P.1
Mumenthaler, C.2
Wuthrich, K.3
-
33
-
-
38549146473
-
Distance dependent centroid to centroid force fields using high resolution decoys
-
DOI 10.1002/prot.21561
-
R. Rajgaria, S. R. McAllister, and C. A. Floudas, Distance dependent centroid to centroid force fields using high resolution decoys, Proteins, vol. 70, pp. 950-970, 2008. (Pubitemid 351161953)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.70
, Issue.3
, pp. 950-970
-
-
Rajgaria, R.1
McAllister, S.R.2
Floudas, C.A.3
-
34
-
-
4444221565
-
UCSF Chimera - A visualization system for exploratory research and analysis
-
E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin, UCSF Chimera - A visualization system for exploratory research and analysis, J. Comput. Chem., vol. 25, pp. 1605-1612, 2004.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
35
-
-
0031862276
-
What should the Z-score of native protein structures be?
-
L. Zhang and J. Skolnick, What should the Z-score of native protein structures be? Protein Sci., vol. 7, pp. 1201-1207, 1998. (Pubitemid 28237053)
-
(1998)
Protein Science
, vol.7
, Issue.5
, pp. 1201-1207
-
-
Zhang, L.I.1
Skolnick, J.2
-
36
-
-
0026723063
-
Protein folding funnels - A kinetic approach to the sequence structure relationship
-
P. E. Leopold, M. Montal, and J. N. Onuchic, Protein folding funnels - A kinetic approach to the sequence structure relationship, Proc. Natl. Acad. Sci. USA, vol. 89, pp. 8721-8725, 1992.
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 8721-8725
-
-
Leopold, P.E.1
Montal, M.2
Onuchic, J.N.3
|