-
1
-
-
0035812694
-
Protein structure prediction and structural genomics
-
DOI 10.1126/science.1065659
-
Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001; 294: 93-96. (Pubitemid 32952955)
-
(2001)
Science
, vol.294
, Issue.5540
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
2
-
-
33644874394
-
MODBASE: A database of annotated comparative protein structure models and associated resources
-
Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 2006; 34: D291-D295.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Pieper, U.1
Eswar, N.2
Davis, F.P.3
Braberg, H.4
Madhusudhan, M.S.5
Rossi, A.6
Marti-Renom, M.7
Karchin, R.8
Webb, B.M.9
Eramian, D.10
Shen, M.Y.11
Kelly, L.12
Melo, F.13
Sali, A.14
-
3
-
-
3242887695
-
Protein structure prediction and analysis using the robetta server
-
DOI 10.1093/nar/gkh468
-
Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 2004; 32: W526-W531. (Pubitemid 38997389)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.WEB. SERVER. ISS.
-
-
Kim, D.E.1
Chivian, D.2
Baker, D.3
-
4
-
-
34548608483
-
Ab initio protein structure prediction using chunk-TASSER
-
DOI 10.1529/biophysj.107.109959
-
Zhou HY, Skolnick J. Ab initio protein structure prediction using Chunk-TASSER. Biophys J 2007; 93: 1510-1518. (Pubitemid 47403296)
-
(2007)
Biophysical Journal
, vol.93
, Issue.5
, pp. 1510-1518
-
-
Zhou, H.1
Skolnick, J.2
-
5
-
-
0242369082
-
RAPTOR optimal protein threading by linear programming
-
Xu J, Li M, Kim D, Xu Y. RAPTOR: optimal protein threading by linear programming. J Bioinform Comput Biol 2003; 1: 95-117.
-
(2003)
J Bioinform Comput Biol
, vol.1
, pp. 95-117
-
-
Xu, J.1
Li, M.2
Kim, D.3
Xu, Y.4
-
7
-
-
0034495586
-
ProSup: A refined tool for protein structure alignment
-
Lackner P, Koppensteiner WA, Sippl MJ, Domingues FS. ProSup: a refined tool for protein structure alignment. Protein. Eng 2000; 13: 745-752. (Pubitemid 32127572)
-
(2000)
Protein Engineering
, vol.13
, Issue.11
, pp. 745-752
-
-
Lackner, P.1
Koppensteiner, W.A.2
Sippl, M.J.3
Domingues, F.S.4
-
8
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
DOI 10.1093/nar/gki524
-
Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005; 33: 2302-2309. (Pubitemid 41439897)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.7
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
9
-
-
0029361476
-
Comparative protein modeling by satisfaction of spatial restraints
-
Sali A. Comparative protein modeling by satisfaction of spatial restraints. Mol Med Today 1995; 1: 270-277.
-
(1995)
Mol Med Today
, vol.1
, pp. 270-277
-
-
Sali, A.1
-
10
-
-
36749030503
-
High accuracy template based modeling by global optimization
-
DOI 10.1002/prot.21628
-
Joo K, Lee J, Lee S, Seo JH, Lee SJ, Lee J. High accuracy template based modeling by global optimization. Proteins 2007; 69: 83-89. (Pubitemid 350210115)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.69
, Issue.SUPPL. 8
, pp. 83-89
-
-
Joo, K.1
Lee, J.2
Lee, S.3
Seo, J.H.4
Sung, J.L.5
Lee, J.6
-
11
-
-
42149153292
-
A multi-template combination algorithm for protein comparative modeling
-
DOI 10.1186/1472-6807-8-18
-
Cheng J. A multi-template combination algorithm for protein comparative modeling. BMC Struct Biol 2008; 8: 18, (Pubitemid 351537916)
-
(2008)
BMC Structural Biology
, vol.8
, pp. 18
-
-
Cheng, J.1
-
12
-
-
0043123123
-
Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments
-
DOI 10.1093/nar/gkg522
-
Poirot O, O'Toole E, Notredame C. Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res 2003; 31: 3503-3506. (Pubitemid 37442186)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3503-3506
-
-
Poirot, O.1
O'Toole, E.2
Notredame, C.3
-
13
-
-
0037406141
-
Can correct protein models be identified?
-
Wallner B, Elofsson A. Can correct protein models be identified? Protein Science 2003; 12: 1073-1086.
-
(2003)
Protein Science
, vol.12
, pp. 1073-1086
-
-
Wallner, B.1
Elofsson, A.2
-
14
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
DOI 10.1110/ps.0217002
-
Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002; 11: 2714-2716; 2003; 12: 2121. (Pubitemid 35191145)
-
(2002)
Protein Science
, vol.11
, Issue.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
15
-
-
50849085804
-
Discriminative learning for protein conformation sampling
-
Zhao F, Li SC, Sterner BW, Xu J. Discriminative learning for protein conformation sampling. Proteins 2008; 73: 228-240.
-
(2008)
Proteins
, vol.73
, pp. 228-240
-
-
Zhao, F.1
Li, S.C.2
Sterner, B.W.3
Xu, J.4
-
16
-
-
67650333594
-
A probabilistic graphical model for Ab initio folding
-
Lecture Notes in Computer Science, Springer
-
Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick and Jinbo Xu. A Probabilistic Graphical Model for Ab Initio Folding, Proc. 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Lecture Notes in Computer Science, Vol. 5541, pp. 59-73, 2009. Springer.
-
(2009)
Proc. 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB)
, vol.5541
, pp. 59-73
-
-
Zhao, F.1
Peng, J.2
Debartolo, J.3
Freed, K.F.4
Sosnick, T.R.5
Xu, J.6
-
17
-
-
0002745702
-
The fisher-bingham distribution on the sphere
-
Kent JT. The fisher-bingham distribution on the sphere. J Roy Stat Soc B 1982; 44: 71-80.
-
(1982)
J Roy Stat Soc B
, vol.44
, pp. 71-80
-
-
Kent, J.T.1
-
19
-
-
34748842218
-
β statistical potentials can outperform all-atom potentials in decoy identification
-
DOI 10.1110/ps.072939707
-
Fitzgerald JE, Jha AK, Colubri A, Sosnick TR, Freed KF. Reduced C-beta statistical potentials can outperform all-atom potentials in decoy identification. Protein Sci 2007; 16: 2123-2139. (Pubitemid 47481648)
-
(2007)
Protein Science
, vol.16
, Issue.10
, pp. 2123-2139
-
-
Fitzgerald, J.E.1
Jha, A.K.2
Colubri, A.3
Sosnick, T.R.4
Freed, K.F.5
-
20
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
DOI 10.1110/ps.062416606
-
Shen M, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006; 15: 2507-2524. (Pubitemid 44771688)
-
(2006)
Protein Science
, vol.15
, Issue.11
, pp. 2507-2524
-
-
Shen, M.1
Sali, A.2
-
21
-
-
2342593131
-
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
-
DOI 10.1073/pnas.0307578101
-
Morozov AV, Kortemme T, Tsemekhman K, Baker D. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci USA 2004; 101: 6946-6951. (Pubitemid 38596423)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.18
, pp. 6946-6951
-
-
Morozov, A.V.1
Kortemme, T.2
Tsemekhman, K.3
Baker, D.4
-
22
-
-
0036971123
-
Dynamics of hydrogen bond desolvation in protein folding
-
DOI 10.1016/S0022-2836(02)00679-4
-
Fernandez A, Sosnick TR, Colubri A. Dynamics of hydrogen bond desolvation in protein folding. J Mol Biol 2002; 321: 659-675. (Pubitemid 36124804)
-
(2002)
Journal of Molecular Biology
, vol.321
, Issue.4
, pp. 659-675
-
-
Fernandez, A.1
Sosnick, T.R.2
Colubri, A.3
-
23
-
-
38549146894
-
The Pfam protein families database
-
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A. The Pfam protein families database. Nucleic Acids Res 2008; 36: D281-D288.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Finn, R.D.1
Tate, J.2
Mistry, J.3
Coggill, P.C.4
Sammut, S.J.5
Hotz, H.R.6
Ceric, G.7
Forslund, K.8
Eddy, S.R.9
Sonnhammer, E.L.10
Bateman, A.11
-
24
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR. Profile hidden Markov models. Bioinformatics 1998; 14: 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
25
-
-
0028181441
-
Hidden markov models in computational biology- Applications to protein modeling
-
DOI 10.1006/jmbi.1994.1104
-
Krogh A, Brown M, Mian IS, Sjolander K, Haussier D. Hidden Markov-models in computational biology-Applications to Protein Modeling. J Mol Biol 1994; 235: 1501-1531. (Pubitemid 2022516)
-
(1994)
Journal of Molecular Biology
, vol.235
, Issue.5
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjolander, K.4
Haussler, D.5
-
26
-
-
84908085765
-
Analysis of casp8 targets, predictions and assessment methods
-
April
-
Shi S, Pei J, Sadreyev RI, Kinch LN, Majumdar I, Tong J, Cheng H, Kim B-H, Grishin NV, "Analysis of casp8 targets, predictions and assessment methods," Database, vol. 2009, no. 0, pp. bap003+, April 2009. [Online]. Available: http://dx.doi.org/10.1093/database/bap003.
-
(2009)
Database
, vol.2009
, Issue.0
-
-
Shi, S.1
Pei, J.2
Sadreyev, R.I.3
Kinch, L.N.4
Majumdar, I.5
Tong, J.6
Cheng, H.7
Kim, B.-H.8
Grishin, N.V.9
-
27
-
-
62849113729
-
SELECTpro: Effective protein model selection using a structure-based energy function resistant to BLUNDERS
-
Randall A, Baldi P. SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERS. BMC Struct Biol 2008; 8: 52.
-
(2008)
BMC Struct Biol
, vol.8
, pp. 52
-
-
Randall, A.1
Baldi, P.2
|