-
1
-
-
67349189383
-
The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain
-
Anfinsen CB, Haber E, Sela M, White F Jr (1961) The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci USA 47(9):1309
-
(1961)
Proc Natl Acad Sci USA
, vol.47
, Issue.9
, pp. 1309
-
-
Anfinsen, C.B.1
Haber, E.2
Sela, M.3
White, F.4
-
2
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5(4):823
-
(1986)
EMBO J
, vol.5
, Issue.4
, pp. 823
-
-
Chothia, C.1
Lesk, A.M.2
-
3
-
-
30444446362
-
Protein‐structure prediction by recombination of fragments
-
Bujnicki JM (2005) Protein‐structure prediction by recombination of fragments. Chembiochem 7(1):19–27
-
(2005)
Chembiochem
, vol.7
, Issue.1
, pp. 19-27
-
-
Bujnicki, J.M.1
-
5
-
-
84995046262
-
A large‐scale experiment to assess protein structure prediction methods
-
Moult J, Pedersen JT, Judson R, Fidelis K (2004) A large‐scale experiment to assess protein structure prediction methods. Proteins 23(3):ii–v
-
(2004)
Proteins
, vol.23
, Issue.3
, pp. ii-iiv
-
-
Moult, J.1
Pedersen, J.T.2
Judson, R.3
Fidelis, K.4
-
6
-
-
42149153292
-
A multi-template combination algorithm for protein comparative modeling
-
Cheng J (2008) A multi-template combination algorithm for protein comparative modeling. BMC Struct Biol 8(1):18
-
(2008)
BMC Struct Biol
, vol.8
, Issue.1
, pp. 18
-
-
Cheng, J.1
-
7
-
-
0037624841
-
3D-SHOTGUN: A novel, cooperative, fold-recognition meta-predictor
-
Fischer D (2003) 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins Struct Funct Bioinf 51(3):434–441
-
(2003)
Proteins Struct Funct Bioinf
, vol.51
, Issue.3
, pp. 434-441
-
-
Fischer, D.1
-
8
-
-
84866909910
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali A, Blundell T (1994) Comparative protein modelling by satisfaction of spatial restraints. Proteins 64:C86
-
(1994)
Proteins
, vol.64
, pp. C86
-
-
Sali, A.1
Blundell, T.2
-
9
-
-
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(7): 882–888
-
(2010)
Bioinformatics
, vol.26
, Issue.7
, pp. 882-888
-
-
Wang, Z.1
Eickholt, J.2
Cheng, J.3
-
10
-
-
74249120024
-
Prediction of global and local quality of CASP8 models by MULTICOM series
-
Cheng J, Wang Z, Tegge AN, Eickholt J (2009) Prediction of global and local quality of CASP8 models by MULTICOM series. Proteins 77(S9):181–184
-
(2009)
Proteins
, vol.77
, Issue.S9
, pp. 181-184
-
-
Cheng, J.1
Wang, Z.2
Tegge, A.N.3
Eickholt, J.4
-
11
-
-
66149156968
-
Evaluating the absolute quality of a single protein model using structural features and support vector machines
-
Wang Z, Tegge AN, Cheng J (2008) Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins 75(3):638–647
-
(2008)
Proteins
, vol.75
, Issue.3
, pp. 638-647
-
-
Wang, Z.1
Tegge, A.N.2
Cheng, J.3
-
12
-
-
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 77(S9):1–4
-
(2009)
Proteins
, vol.77
, Issue.S9
, pp. 1-4
-
-
Moult, J.1
Fidelis, K.2
Kryshtafovych, A.3
Rost, B.4
Tramontano, A.5
-
13
-
-
4444221565
-
UCSF Chimera: A visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera: a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612
-
(2004)
J Comput Chem
, vol.25
, Issue.13
, 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
-
14
-
-
84941038657
-
-
LLC DS The PyMOL molecular graphics system
-
LLC DS The PyMOL molecular graphics system. http://pymol.sourceforge.net/
-
-
-
-
15
-
-
84941122621
-
-
RasMol v2. 5-Molecular visualization program
-
Sayle R (1994) RasMol v2. 5-Molecular visualization program
-
(1994)
-
-
Sayle, R.1
-
16
-
-
84941064874
-
-
Jmol: an open-source Java viewer for chemical structures in 3D, Accessed 10 Dec
-
Jmol: an open-source Java viewer for chemical structures in 3D. http://jmol.sourceforge.net/. Accessed 10 Dec 2008
-
(2008)
-
-
-
17
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang Y, Skolnick J (2004) Scoring function for automated assessment of protein structure template quality. Proteins 57(4):702–710
-
(2004)
Proteins
, vol.57
, Issue.4
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
18
-
-
84874240142
-
Designing and benchmarking the MULTICOM protein structure prediction system
-
Li J, Deng X, Eickholt J, Cheng J (2013) Designing and benchmarking the MULTICOM protein structure prediction system. BMC Struct Biol 13:2
-
(2013)
BMC Struct Biol
, vol.13
, pp. 2
-
-
Li, J.1
Deng, X.2
Eickholt, J.3
Cheng, J.4
-
19
-
-
0033954256
-
The protein data bank
-
Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P (2000) The protein data bank. Nucleic Acids Res 28(1):235–242
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.5
Weissig, H.6
Shindyalov, I.7
Bourne, P.8
-
20
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
21
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S, Gish W, Miller W, Myers E, Lipman D (1990) Basic local alignment search tool. J mol Biol 215(3):403–410
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.1
Gish, W.2
Miller, W.3
Myers, E.4
Lipman, D.5
-
22
-
-
62649147821
-
Sequence contextspecific profiles for homology searching
-
Biegert A, Söding J (2009) Sequence contextspecific profiles for homology searching. Proc Natl Acad Sci USA 106(10):3770–3775
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.10
, pp. 3770-3775
-
-
Biegert, A.1
Söding, J.2
-
24
-
-
79959931985
-
HMMER web server: Interactive sequence similarity searching
-
Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39(Suppl 2):W29–W37
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W29-W37
-
-
Finn, R.D.1
Clements, J.2
Eddy, S.R.3
-
25
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
Soding J, Biegert A, Lupas A (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server Issue):W244–W248
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.Web Server Issue
, pp. W244-W248
-
-
Soding, J.1
Biegert, A.2
Lupas, A.3
-
26
-
-
84941032363
-
-
the profile comparer
-
PRC, the profile comparer. http://supfam.org/PRC/
-
-
-
-
27
-
-
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(1):317–336
-
(2003)
J Mol Biol
, vol.326
, Issue.1
, pp. 317-336
-
-
Sadreyev, R.1
Grishin, N.2
-
28
-
-
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 Res 33(7):2302–2309
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.7
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
29
-
-
24644512819
-
SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures
-
Zhou H, Zhou Y (2005) SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics 21(18):3615–3621
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3615-3621
-
-
Zhou, H.1
Zhou, Y.2
-
30
-
-
0347383758
-
Modeller: Generation and refinement of homology-based protein structure models
-
Fiser A, Sali A (2003) Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374:461–491
-
(2003)
Methods Enzymol
, vol.374
, pp. 461-491
-
-
Fiser, A.1
Sali, A.2
-
31
-
-
84862972847
-
Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9
-
IEEE
-
Cheng J, Wang Z, Eickholt J, Deng X (2011) Recursive protein modeling: a divide and conquer strategy for protein structure prediction and its case study in CASP9. In: Bioinformatics and Biomedicine Workshops (BIBMW). IEEE. p 352–357
-
(2011)
Bioinformatics and Biomedicine Workshops (BIBMW)
, pp. 352-357
-
-
Cheng, J.1
Wang, Z.2
Eickholt, J.3
Deng, X.4
-
32
-
-
78650905964
-
ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
-
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487:545–574
-
(2011)
Methods Enzymol
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
Tyka, M.2
Lewis, S.M.3
Lange, O.F.4
Thompson, J.5
Jacak, R.6
Kaufman, K.7
Renfrew, P.D.8
Smith, C.A.9
Sheffler, W.10
-
33
-
-
66149156968
-
Evaluating the absolute quality of a single protein model using structural features and support vector machines
-
Wang Z, Tegge AN, Cheng J (2009) Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins 75(3):638–647
-
(2009)
Proteins
, vol.75
, Issue.3
, pp. 638-647
-
-
Wang, Z.1
Tegge, A.N.2
Cheng, J.3
-
34
-
-
23144465987
-
SCRATCH: A protein structure and structural feature prediction server
-
Cheng J, Randall A, Sweredoski M, Baldi P (2005) SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 33(Web Server Issue):W72–W76
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.Web Server Issue
, pp. W72-W76
-
-
Cheng, J.1
Randall, A.2
Sweredoski, M.3
Baldi, P.4
-
35
-
-
67849110005
-
NNcon: Improved protein contact map prediction using 2D-recursive neural networks
-
Tegge AN, Wang Z, Eickholt J, Cheng J (2009) NNcon: improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Res 37(Suppl 2):W515–W518
-
(2009)
Nucleic Acids Res
, vol.37
, pp. W515-W518
-
-
Tegge, A.N.1
Wang, Z.2
Eickholt, J.3
Cheng, J.4
-
36
-
-
84860507958
-
Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms
-
Cheng J, Baldi P (2005) Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms. Bioinformatics 21(Suppl 1):i75–i84
-
(2005)
Bioinformatics
, vol.21
, pp. i75-i84
-
-
Cheng, J.1
Baldi, P.2
|