-
1
-
-
0031564630
-
A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence
-
Rice DW, Eisenberg D, (1997) A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J Mol Biol 267: 1026-1038.
-
(1997)
J Mol Biol
, vol.267
, pp. 1026-1038
-
-
Rice, D.W.1
Eisenberg, D.2
-
2
-
-
0033537993
-
GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
-
Jones DT, (1999) GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. Journal of Molecular Biology 287: 797-815.
-
(1999)
Journal of Molecular Biology
, vol.287
, pp. 797-815
-
-
Jones, D.T.1
-
3
-
-
0035967880
-
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi J, Blundell TL, Mizuguchi K, (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 310: 243-257.
-
(2001)
J Mol Biol
, vol.310
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
4
-
-
0036681387
-
A novel fold recognition method using composite predicted secondary structures
-
An YL, Friesner RA, (2002) A novel fold recognition method using composite predicted secondary structures. Proteins-Structure Function and Genetics 48: 352-366.
-
(2002)
Proteins-Structure Function and Genetics
, vol.48
, pp. 352-366
-
-
An, Y.L.1
Friesner, R.A.2
-
5
-
-
0038386050
-
3D-Jury: a simple approach to improve protein structure predictions
-
Ginalski K, Elofsson A, Fischer D, Rychlewski L, (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19: 1015-1018.
-
(2003)
Bioinformatics
, vol.19
, pp. 1015-1018
-
-
Ginalski, K.1
Elofsson, A.2
Fischer, D.3
Rychlewski, L.4
-
6
-
-
0242369082
-
RAPTOR: optimal protein threading by linear programming
-
Xu J, Li M, Kim D, Xu Y, (2003) RAPTOR: optimal protein threading by linear programming. J Bioinform Comput Biol 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
-
-
2542631929
-
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
-
Zhou H, Zhou Y, (2004) Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 55: 1005-1013.
-
(2004)
Proteins
, vol.55
, pp. 1005-1013
-
-
Zhou, H.1
Zhou, Y.2
-
8
-
-
17144425763
-
Practical lessons from protein structure prediction
-
Ginalski K, Grishin NV, Godzik A, Rychlewski L, (2005) Practical lessons from protein structure prediction. Nucleic Acids Res 33: 1874-1891.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1874-1891
-
-
Ginalski, K.1
Grishin, N.V.2
Godzik, A.3
Rychlewski, L.4
-
9
-
-
11344292852
-
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
-
Zhou HY, Zhou YQ, (2005) Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins-Structure Function and Bioinformatics 58: 321-328.
-
(2005)
Proteins-Structure Function and Bioinformatics
, vol.58
, pp. 321-328
-
-
Zhou, H.Y.1
Zhou, Y.Q.2
-
10
-
-
34447506573
-
Fold recognition by concurrent use of solvent accessibility and residue depth
-
Liu S, Zhang C, Liang SD, Zhou YQ, (2007) Fold recognition by concurrent use of solvent accessibility and residue depth. Proteins-Structure Function and Bioinformatics 68: 636-645.
-
(2007)
Proteins-Structure Function and Bioinformatics
, vol.68
, pp. 636-645
-
-
Liu, S.1
Zhang, C.2
Liang, S.D.3
Zhou, Y.Q.4
-
11
-
-
48449085801
-
SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model
-
Zhang W, Liu S, Zhou YQ, (2008) SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model. PLoS One 3: e2325.
-
(2008)
PLoS One
, vol.3
-
-
Zhang, W.1
Liu, S.2
Zhou, Y.Q.3
-
12
-
-
23144463912
-
FFAS03: a server for profile-profile sequence alignments
-
Jaroszewski L, Rychlewski L, Li ZW, Li WZ, Godzik A, (2005) FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Research 33: W284-W288.
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Jaroszewski, L.1
Rychlewski, L.2
Li, Z.W.3
Li, W.Z.4
Godzik, A.5
-
13
-
-
35748965848
-
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
-
Fernandez-Fuentes N, Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A, (2007) Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments. Bioinformatics 23: 2558-2565.
-
(2007)
Bioinformatics
, vol.23
, pp. 2558-2565
-
-
Fernandez-Fuentes, N.1
Rai, B.K.2
Madrid-Aliste, C.J.3
Fajardo, J.E.4
Fiser, A.5
-
14
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
15
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR, (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
16
-
-
0038634975
-
Improvement of the GenTHREADER method for genomic fold recognition
-
McGuffin LJ, Jones DT, (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19: 874-881.
-
(2003)
Bioinformatics
, vol.19
, pp. 874-881
-
-
McGuffin, L.J.1
Jones, D.T.2
-
17
-
-
0042121000
-
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure
-
Ginalski K, Pas J, Wyrwicz LS, von Grotthuss M, Bujnicki JM, et al. (2003) ORFeus: detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Research 31: 3804-3807.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 3804-3807
-
-
Ginalski, K.1
Pas, J.2
Wyrwicz, L.S.3
von Grotthuss, M.4
Bujnicki, J.M.5
-
18
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Soding J, (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21: 951-960.
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Soding, J.1
-
19
-
-
46449123146
-
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
-
Wu ST, Zhang Y, (2008) MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins-Structure Function and Bioinformatics 72: 547-556.
-
(2008)
Proteins-Structure Function and Bioinformatics
, vol.72
, pp. 547-556
-
-
Wu, S.T.1
Zhang, Y.2
-
20
-
-
0034628922
-
Combination of threading potentials and sequence profiles improves fold recognition
-
Panchenko AR, Marchler-Bauer A, Bryant SH, (2000) Combination of threading potentials and sequence profiles improves fold recognition. J Mol Biol 296: 1319-1331.
-
(2000)
J Mol Biol
, vol.296
, pp. 1319-1331
-
-
Panchenko, A.R.1
Marchler-Bauer, A.2
Bryant, S.H.3
-
21
-
-
0038278386
-
Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry
-
Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K, (2003) Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry. Proteins-Structure Function and Bioinformatics 51: 504-514.
-
(2003)
Proteins-Structure Function and Bioinformatics
, vol.51
, pp. 504-514
-
-
Karchin, R.1
Cline, M.2
Mandel-Gutfreund, Y.3
Karplus, K.4
-
22
-
-
24144437430
-
Improving sequence-based fold recognition by using 3D model quality assessment
-
Pettitt CS, McGuffin LJ, Jones DT, (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.S.1
McGuffin, L.J.2
Jones, D.T.3
-
23
-
-
39749141523
-
Assessing the reliability of sequence similarities detected through hydrophobic cluster analysis
-
Silva PJ, (2008) Assessing the reliability of sequence similarities detected through hydrophobic cluster analysis. Proteins 70: 1588-1594.
-
(2008)
Proteins
, vol.70
, pp. 1588-1594
-
-
Silva, P.J.1
-
24
-
-
77953581940
-
Improving threading algorithms for remote homology modeling by combining fragment and template comparisons
-
Zhou H, Skolnick J, (2010) Improving threading algorithms for remote homology modeling by combining fragment and template comparisons. Proteins 78: 2041-2048.
-
(2010)
Proteins
, vol.78
, pp. 2041-2048
-
-
Zhou, H.1
Skolnick, J.2
-
25
-
-
3242889054
-
Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices
-
Torda AE, Procter JB, Huber T, (2004) Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. Nucleic Acids Res 32: W532-535.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Torda, A.E.1
Procter, J.B.2
Huber, T.3
-
26
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD, (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
27
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith TF, Waterman MS, (1981) Identification of common molecular subsequences. J Mol Biol 147: 195-197.
-
(1981)
J Mol Biol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
28
-
-
0027136282
-
Comparative Protein Modeling by Satisfaction of Spatial Restraints
-
Sali A, Blundell TL, (1993) Comparative Protein Modeling by Satisfaction of Spatial Restraints. Journal of Molecular Biology 234: 779-815.
-
(1993)
Journal of Molecular Biology
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
30
-
-
17644392830
-
TM-align: a protein structure alignment algorithm based on the TM-score
-
Zhang Y, Skolnick J, (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Research 33: 2302-2309.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
31
-
-
0034695414
-
Identification of related proteins on family, superfamily and fold level
-
Lindahl E, Elofsson A, (2000) Identification of related proteins on family, superfamily and fold level. J Mol Biol 295: 613-625.
-
(2000)
J Mol Biol
, vol.295
, pp. 613-625
-
-
Lindahl, E.1
Elofsson, A.2
-
32
-
-
33745616114
-
A machine learning information retrieval approach to protein fold recognition
-
Cheng J, Baldi P, (2006) A machine learning information retrieval approach to protein fold recognition. Bioinformatics 22: 1456-1463.
-
(2006)
Bioinformatics
, vol.22
, pp. 1456-1463
-
-
Cheng, J.1
Baldi, P.2
-
33
-
-
74049119478
-
DescFold: A web server for protein fold recognition
-
Yan RX, Si JN, Wang C, Zhang ZD, (2009) DescFold: A web server for protein fold recognition. BMC Bioinformatics 10: 416.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 416
-
-
Yan, R.X.1
Si, J.N.2
Wang, C.3
Zhang, Z.D.4
-
34
-
-
74249119329
-
Critical assessment of methods of protein structure prediction-Round VIII
-
Moult J, Fidelis K, Kryshtafovych A, Rost B, Tramontano A, (2009) Critical assessment of methods of protein structure prediction-Round VIII. Proteins-Structure Function and Bioinformatics 77: 1-4.
-
(2009)
Proteins-Structure Function and Bioinformatics
, vol.77
, pp. 1-4
-
-
Moult, J.1
Fidelis, K.2
Kryshtafovych, A.3
Rost, B.4
Tramontano, A.5
-
36
-
-
0032214622
-
Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules
-
Sussman JL, Lin DW, Jiang JS, Manning NO, Prilusky J, et al. (1998) Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules. Acta Crystallographica Section D-Biological Crystallography 54: 1078-1084.
-
(1998)
Acta Crystallographica Section D-Biological Crystallography
, vol.54
, pp. 1078-1084
-
-
Sussman, J.L.1
Lin, D.W.2
Jiang, J.S.3
Manning, N.O.4
Prilusky, J.5
-
37
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
38
-
-
0037423702
-
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance
-
Sadreyev R, Grishin N, (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol 326: 317-336.
-
(2003)
J Mol Biol
, vol.326
, pp. 317-336
-
-
Sadreyev, R.1
Grishin, N.2
-
39
-
-
42649142258
-
Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms
-
Poleksic A, Fienup M, (2008) Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms. Bioinformatics 24: 1145-1153.
-
(2008)
Bioinformatics
, vol.24
, pp. 1145-1153
-
-
Poleksic, A.1
Fienup, M.2
-
40
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus K, Barrett C, Hughey R, (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics 14: 846-856.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
41
-
-
0034780030
-
Pcons: A neural-network-based consensus predictor that improves fold recognition
-
Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A, (2001) Pcons: A neural-network-based consensus predictor that improves fold recognition. Protein Science 10: 2354-2362.
-
(2001)
Protein Science
, vol.10
, pp. 2354-2362
-
-
Lundstrom, J.1
Rychlewski, L.2
Bujnicki, J.3
Elofsson, A.4
-
42
-
-
34250851687
-
LOMETS: a local meta-threading-server for protein structure prediction
-
Wu S, Zhang Y, (2007) LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 35: 3375-3382.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3375-3382
-
-
Wu, S.1
Zhang, Y.2
-
43
-
-
38549141229
-
Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre
-
Bennett-Lovsey RM, Herbert AD, Sternberg MJE, Kelley LA, (2008) Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins-Structure Function and Bioinformatics 70: 611-625.
-
(2008)
Proteins-Structure Function and Bioinformatics
, vol.70
, pp. 611-625
-
-
Bennett-Lovsey, R.M.1
Herbert, A.D.2
Sternberg, M.J.E.3
Kelley, L.A.4
-
44
-
-
34547574147
-
M4T: a comparative protein structure modeling server
-
Fernandez-Fuentes N, Madrid-Aliste CJ, Rai BK, Fajardo JE, Fiser A, (2007) M4T: a comparative protein structure modeling server. Nucleic Acids Res 35: W363-368.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Fernandez-Fuentes, N.1
Madrid-Aliste, C.J.2
Rai, B.K.3
Fajardo, J.E.4
Fiser, A.5
-
45
-
-
74249111445
-
Template-based and free modeling by RAPTOR++ in CASP8
-
Xu J, Peng J, Zhao F, (2009) Template-based and free modeling by RAPTOR++ in CASP8. Proteins 77 (Suppl 9): 133-137.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 133-137
-
-
Xu, J.1
Peng, J.2
Zhao, F.3
-
46
-
-
74249106219
-
I-TASSER: fully automated protein structure prediction in CASP8
-
Zhang Y, (2009) I-TASSER: fully automated protein structure prediction in CASP8. Proteins 77 (Suppl 9): 100-113.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 100-113
-
-
Zhang, Y.1
-
47
-
-
77951941264
-
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8
-
Wang Z, Eickholt J, Cheng J, (2010) MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics 26: 882-888.
-
(2010)
Bioinformatics
, vol.26
, pp. 882-888
-
-
Wang, Z.1
Eickholt, J.2
Cheng, J.3
-
48
-
-
36749055649
-
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
-
Das R, Qian B, Raman S, Vernon R, Thompson J, et al. (2007) Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 69 (Suppl 8): 118-128.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 118-128
-
-
Das, R.1
Qian, B.2
Raman, S.3
Vernon, R.4
Thompson, J.5
-
49
-
-
71649097064
-
FAMSD: A Powerful Protein Modeling Platform that Combines Alignment Methods, Homology Modeling, 3D Structure Quality Estimation and Molecular Dynamics
-
Kanou K, Iwadate M, Hirata T, Terashi G, Umeyama H, et al. (2009) FAMSD: A Powerful Protein Modeling Platform that Combines Alignment Methods, Homology Modeling, 3D Structure Quality Estimation and Molecular Dynamics. Chemical & Pharmaceutical Bulletin 57: 1335-1342.
-
(2009)
Chemical & Pharmaceutical Bulletin
, vol.57
, pp. 1335-1342
-
-
Kanou, K.1
Iwadate, M.2
Hirata, T.3
Terashi, G.4
Umeyama, H.5
-
50
-
-
34548608483
-
Ab initio protein structure prediction using chunk-TASSER
-
Zhou H, Skolnick J, (2007) Ab initio protein structure prediction using chunk-TASSER. Biophys J 93: 1510-1518.
-
(2007)
Biophys J
, vol.93
, pp. 1510-1518
-
-
Zhou, H.1
Skolnick, J.2
-
51
-
-
0033405214
-
Hidden Markov model approach for identifying the modular framework of the protein backbone
-
Camproux AC, Tuffery P, Chevrolat JP, Boisvieux JF, Hazout S, (1999) Hidden Markov model approach for identifying the modular framework of the protein backbone. Protein Eng 12: 1063-1073.
-
(1999)
Protein Eng
, vol.12
, pp. 1063-1073
-
-
Camproux, A.C.1
Tuffery, P.2
Chevrolat, J.P.3
Boisvieux, J.F.4
Hazout, S.5
-
54
-
-
2442592993
-
A hidden markov model derived structural alphabet for proteins
-
Camproux AC, Gautier R, Tuffery P, (2004) A hidden markov model derived structural alphabet for proteins. J Mol Biol 339: 591-605.
-
(2004)
J Mol Biol
, vol.339
, pp. 591-605
-
-
Camproux, A.C.1
Gautier, R.2
Tuffery, P.3
-
55
-
-
33144460796
-
Local protein structure prediction using discriminative models
-
Sander O, Sommer I, Lengauer T, (2006) Local protein structure prediction using discriminative models. BMC Bioinformatics 7: 14.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 14
-
-
Sander, O.1
Sommer, I.2
Lengauer, T.3
-
56
-
-
48249155051
-
A generative, probabilistic model of local protein structure
-
Boomsma W, Mardia KV, Taylor CC, Ferkinghoff-Borg J, Krogh A, et al. (2008) A generative, probabilistic model of local protein structure. Proceedings of the National Academy of Sciences of the United States of America 105: 8932-8937.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, pp. 8932-8937
-
-
Boomsma, W.1
Mardia, K.V.2
Taylor, C.C.3
Ferkinghoff-Borg, J.4
Krogh, A.5
-
58
-
-
54249084066
-
LOCUSTRA: Accurate prediction of local protein structure using a two-layer support vector machine approach
-
Zimmermann O, Hansmann UHE, (2008) LOCUSTRA: Accurate prediction of local protein structure using a two-layer support vector machine approach. Journal of Chemical Information and Modeling 48: 1903-1908.
-
(2008)
Journal of Chemical Information and Modeling
, vol.48
, pp. 1903-1908
-
-
Zimmermann, O.1
Hansmann, U.H.E.2
-
59
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons KT, Kooperberg C, Huang E, Baker D, (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.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
60
-
-
0344033670
-
Efficient remote homology detection using local structure
-
Hou Y, Hsu W, Lee ML, Bystroff C, (2003) Efficient remote homology detection using local structure. Bioinformatics 19: 2294-2301.
-
(2003)
Bioinformatics
, vol.19
, pp. 2294-2301
-
-
Hou, Y.1
Hsu, W.2
Lee, M.L.3
Bystroff, C.4
-
61
-
-
33846104376
-
All-atom ab initio folding of a diverse set of proteins
-
Yang JS, Chen WW, Skolnick J, Shakhnovich EI, (2007) All-atom ab initio folding of a diverse set of proteins. Structure 15: 53-63.
-
(2007)
Structure
, vol.15
, pp. 53-63
-
-
Yang, J.S.1
Chen, W.W.2
Skolnick, J.3
Shakhnovich, E.I.4
-
62
-
-
0038451355
-
Reduction of protein sequence complexity by residue grouping
-
Li TP, Fan K, Wang J, Wang W, (2003) Reduction of protein sequence complexity by residue grouping. Protein Engineering 16: 323-330.
-
(2003)
Protein Engineering
, vol.16
, pp. 323-330
-
-
Li, T.P.1
Fan, K.2
Wang, J.3
Wang, W.4
-
63
-
-
0041843696
-
TOUCHSTONE II: a new approach to ab initio protein structure prediction
-
Zhang Y, Kolinski A, Skolnick J, (2003) TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 85: 1145-1164.
-
(2003)
Biophys J
, vol.85
, pp. 1145-1164
-
-
Zhang, Y.1
Kolinski, A.2
Skolnick, J.3
-
64
-
-
44449124693
-
Fast procedure for reconstruction of full-atom protein models from reduced representations
-
Rotkiewicz P, Skolnick J, (2008) Fast procedure for reconstruction of full-atom protein models from reduced representations. J Comput Chem 29: 1460-1465.
-
(2008)
J Comput Chem
, vol.29
, pp. 1460-1465
-
-
Rotkiewicz, P.1
Skolnick, J.2
-
65
-
-
0043180474
-
PISCES: a protein sequence culling server
-
Wang G, Dunbrack RL Jr, (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
66
-
-
0034495586
-
ProSup: a refined tool for protein structure alignment
-
Lackner P, Koppensteiner WA, Sippl MJ, Domingues FS, (2000) ProSup: a refined tool for protein structure alignment. Protein Engineering 13: 745-752.
-
(2000)
Protein Engineering
, vol.13
, pp. 745-752
-
-
Lackner, P.1
Koppensteiner, W.A.2
Sippl, M.J.3
Domingues, F.S.4
-
67
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT, (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195-202.
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
68
-
-
0020997912
-
Dictionary of Protein Secondary Structure - Pattern-Recognition of Hydrogen-Bonded and Geometrical Features
-
Kabsch W, Sander C, (1983) Dictionary of Protein Secondary Structure- Pattern-Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers 22: 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
69
-
-
77954196482
-
Low-homology protein threading
-
Peng J, Xu J, (2010) Low-homology protein threading. Bioinformatics 26: i294-300.
-
(2010)
Bioinformatics
, vol.26
-
-
Peng, J.1
Xu, J.2
|