-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul,S.F. 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
-
2
-
-
36749103110
-
Automated server predictions in CASP7
-
Battey,J.N.D. et al. (2007) Automated server predictions in CASP7. Proteins, 69 (Suppl. 8), 68-82.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 68-82
-
-
Battey, J.N.D.1
-
3
-
-
38549141229
-
Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre
-
Bennett-Lovsey,R.M. et al. (2008) Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins, 70, 611-625.
-
(2008)
Proteins
, vol.70
, pp. 611-625
-
-
Bennett-Lovsey, R.M.1
-
4
-
-
30444446362
-
Protein-structure prediction by recombination of fragments
-
Bujnicki,J.M. (2006) Protein-structure prediction by recombination of fragments. Chembiochem, 7, 19-27.
-
(2006)
Chembiochem
, vol.7
, pp. 19-27
-
-
Bujnicki, J.M.1
-
5
-
-
33745616114
-
A machine learning information retrieval approach to protein fold recognition
-
Cheng,J. and 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
-
6
-
-
10744230917
-
Automated prediction of CASP-5 structures using the robetta server
-
Chivian,D. et al. (2003) Automated prediction of CASP-5 structures using the robetta server. Proteins, 53 (Suppl. 6), 524-533.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 524-533
-
-
Chivian, D.1
-
7
-
-
79953873680
-
Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations
-
Dai,L. and Zhou,Y. (2011) Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations. J. Mol. Biol., 408, 585-595.
-
(2011)
J. Mol. Biol.
, vol.408
, pp. 585-595
-
-
Dai, L.1
Zhou, Y.2
-
8
-
-
0034615787
-
Structure-based evaluation of sequence comparison and fold recognition alignment accuracy
-
Domingues,F.S. et al. (2000) Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J. Mol. Biol., 297, 1003-1013.
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 1003-1013
-
-
Domingues, F.S.1
-
9
-
-
33847073796
-
Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training
-
Dor,O. and Zhou,Y. (2007) Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training. Proteins, 66, 838-845.
-
(2007)
Proteins
, vol.66
, pp. 838-845
-
-
Dor, O.1
Zhou, Y.2
-
10
-
-
61449123967
-
Improving the accuracy of predicting real-value backbone torsion angles and residue solvent accessibility by guided learning through two-layer neural networks
-
Faraggi,E. et al. (2009a) Improving the accuracy of predicting real-value backbone torsion angles and residue solvent accessibility by guided learning through two-layer neural networks. Proteins, 74, 847-856.
-
(2009)
Proteins
, vol.74
, pp. 847-856
-
-
Faraggi, E.1
-
11
-
-
70350738241
-
Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction
-
Faraggi,E. et al. (2009b) Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction. Structure, 17, 1515-1527.
-
(2009)
Structure
, vol.17
, pp. 1515-1527
-
-
Faraggi, E.1
-
13
-
-
0033168498
-
Hidden markov models that use predicted secondary structures for fold recognition
-
Hargbo,J. and Elofsson,A. (1999) Hidden markov models that use predicted secondary structures for fold recognition. Proteins, 36, 68-76.
-
(1999)
Proteins
, vol.36
, pp. 68-76
-
-
Hargbo, J.1
Elofsson, A.2
-
14
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones,D.T. (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
-
15
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch,W. and 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
-
16
-
-
0242720595
-
The PDB is a covering set of small protein structures
-
Kihara,D. and Skolnick,J. (2003) The PDB is a covering set of small protein structures. J. Mol. Biol., 334, 793-802.
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 793-802
-
-
Kihara, D.1
Skolnick, J.2
-
17
-
-
0142184275
-
PROSPECT II: protein structure prediction program for the genome-scale
-
Kim,D. et al. (2003) PROSPECT II: protein structure prediction program for the genome-scale. Protein Eng., 16, 641-650.
-
(2003)
Protein Eng.
, vol.16
, pp. 641-650
-
-
Kim, D.1
-
18
-
-
0034695414
-
Identification of related proteins on family, superfamily and fold level
-
Lindahl,E. and 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
-
19
-
-
34447506573
-
Fold recognition by concurrent use of solvent accessibility and residue depth
-
Liu,S. et al. (2007) Fold recognition by concurrent use of solvent accessibility and residue depth. Proteins, 68, 636-645.
-
(2007)
Proteins
, vol.68
, pp. 636-645
-
-
Liu, S.1
-
20
-
-
67649887151
-
pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination
-
Lobley,A. et al. (2009) pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinformatics, 25, 1761-1767.
-
(2009)
Bioinformatics
, vol.25
, pp. 1761-1767
-
-
Lobley, A.1
-
21
-
-
55749113550
-
Profile comparer (prc): a program for scoring and aligning profile hidden markov models
-
Madera,M. (2008) Profile comparer (prc): a program for scoring and aligning profile hidden markov models. Bioinformatics, 24, 2630-2631.
-
(2008)
Bioinformatics
, vol.24
, pp. 2630-2631
-
-
Madera, M.1
-
22
-
-
1842559320
-
Alignment of protein sequences by their profiles
-
Marti-Renom,M.A. et al. (2004) Alignment of protein sequences by their profiles. Protein Sci., 13, 1071-1087.
-
(2004)
Protein Sci.
, vol.13
, pp. 1071-1087
-
-
Marti-Renom, M.A.1
-
23
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin,A.G. et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
-
25
-
-
77954196482
-
Low-homology protein threading
-
Peng,J. and Xu,J. (2010) Low-homology protein threading. Bioinformatics, 26, i294-i300.
-
(2010)
Bioinformatics
, vol.26
-
-
Peng, J.1
Xu, J.2
-
26
-
-
0004161838
-
-
2nd edn. Cambridge University Press, Cambridge, UK
-
Press,W. et al. (1992) Numerical Recipes in C. 2nd edn. Cambridge University Press, Cambridge, UK.
-
(1992)
Numerical Recipes in C
-
-
Press, W.1
-
27
-
-
0031577260
-
Protein fold recognition by prediction-based threading
-
Rost,B. et al. (1997) Protein fold recognition by prediction-based threading J. Mol. Biol., 270, 471-480.
-
(1997)
J. Mol. Biol.
, vol.270
, pp. 471-480
-
-
Rost, B.1
-
28
-
-
0028871814
-
Evaluation of comparative protein modelling by MODELLER
-
Sali,A. et al. (1995) Evaluation of comparative protein modelling by MODELLER. Proteins, 23, 318-326.
-
(1995)
Proteins
, vol.23
, pp. 318-326
-
-
Sali, A.1
-
29
-
-
0035967880
-
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi,J. et al. (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
-
30
-
-
0033670439
-
Maxsub: an automated measure for the assessment of protein structure prediction quality
-
Siew,N. et al. (2000) Maxsub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics, 16, 776-785.
-
(2000)
Bioinformatics
, vol.16
, pp. 776-785
-
-
Siew, N.1
-
31
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith,T.F. and Waterman,M.S. (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
-
32
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
Soding,J. et al. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33, W244-W248.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Soding, J.1
-
33
-
-
36749027045
-
Fams-ace: a combined method to select the best model after remodeling all server models
-
Terashi,G. et al. (2007) Fams-ace: a combined method to select the best model after remodeling all server models. Proteins, 69 (Suppl. 8), 98-107.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 98-107
-
-
Terashi, G.1
-
34
-
-
30344447955
-
Assessment of predictions submitted for the CASP6 comparative modeling category
-
Tress,M. et al. (2005) Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins, 61 (Suppl. 7), 27-45.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 27-45
-
-
Tress, M.1
-
35
-
-
34547612652
-
Pcons.net: protein structure prediction meta server
-
Wallner,B. et al. (2007) Pcons.net: protein structure prediction meta server. Nucleic Acids Res., 35, W369-W374.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Wallner, B.1
-
36
-
-
46449123146
-
MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information
-
Wu,S. and Zhang,Y. (2008) MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins, 72, 547-556.
-
(2008)
Proteins
, vol.72
, pp. 547-556
-
-
Wu, S.1
Zhang, Y.2
-
37
-
-
0242338315
-
Protein structure prediction by linear programming
-
Xu,J. et al. (2003) Protein structure prediction by linear programming. Pac. Symp. Biocomput., 8, 264-275.
-
(2003)
Pac. Symp. Biocomput.
, vol.8
, pp. 264-275
-
-
Xu, J.1
-
38
-
-
46449139781
-
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely-related all-atom statistical energy functions
-
Yang,Y. and Zhou,Y. (2008) Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely-related all-atom statistical energy functions. Protein Sci., 17, 1212-1219.
-
(2008)
Protein Sci.
, vol.17
, pp. 1212-1219
-
-
Yang, Y.1
Zhou, Y.2
-
39
-
-
36749061828
-
Template-based modeling and free modeling by I-TASSER in CASP7
-
Zhang,Y. (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins Suppl., 69, 108-117.
-
(2007)
Proteins Suppl.
, vol.69
, pp. 108-117
-
-
Zhang, Y.1
-
40
-
-
17644392830
-
TM-align: a protein structure alignment algorithm based on the TM-score
-
Zhang,Y. and Skolnick,J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302-2309.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
41
-
-
33644553089
-
On the origin and completeness of single domain structures
-
Zhang,Y. et al. (2006) On the origin and completeness of single domain structures. Proc. Natl Acad. Sci., 103, 2605-2610.
-
(2006)
Proc. Natl Acad. Sci.
, vol.103
, pp. 2605-2610
-
-
Zhang, Y.1
-
42
-
-
48449085801
-
SP5: improving protein fold recognition by using predicted torsion angles and profile-based gap penalty
-
Zhang,W. et al. (2008) SP5: improving protein fold recognition by using predicted torsion angles and profile-based gap penalty. PLoS One, 6, e2325.
-
(2008)
PLoS One
, vol.6
-
-
Zhang, W.1
-
43
-
-
77953581940
-
Improving threading algorithms for remote homology modeling by combining fragment and template comparisons
-
Zhou,H. and 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
-
44
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou,H. and Zhou, Y. (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci., 11, 2714-2726.
-
(2002)
Protein Sci.
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
45
-
-
2542631929
-
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
-
Zhou,H. and 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
-
46
-
-
11344292852
-
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
-
Zhou,H. and Zhou,Y. (2005a) Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins, 58, 321-328.
-
(2005)
Proteins
, vol.58
, pp. 321-328
-
-
Zhou, H.1
Zhou, Y.2
-
47
-
-
30344456694
-
SPARKS 2 and SP3 servers in CASP 6
-
Zhou,H. and Zhou,Y. (2005b) SPARKS 2 and SP3 servers in CASP 6. Proteins, 61 (Suppl. 7), 152-156.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 152-156
-
-
Zhou, H.1
Zhou, Y.2
-
48
-
-
36749095600
-
Analysis of TASSER-based CASP7 protein structure prediction results
-
Zhou,H. et al. (2007a) Analysis of TASSER-based CASP7 protein structure prediction results. Proteins, 69 (Suppl. 8), 90-97.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 90-97
-
-
Zhou, H.1
-
49
-
-
34247619229
-
DDOMAIN: dividing structures into domains using a normalized domain-domain interaction profile
-
Zhou,H. et al. (2007b) DDOMAIN: dividing structures into domains using a normalized domain-domain interaction profile. Protein Sci., 16, 947-955.
-
(2007)
Protein Sci.
, vol.16
, pp. 947-955
-
-
Zhou, H.1
-
50
-
-
79251601609
-
Trends in template/fragment-free protein structure prediction
-
Zhou,Y. et al. (2010) Trends in template/fragment-free protein structure prediction. Theor. Chem. Acc., 128, 3-16.
-
(2010)
Theor. Chem. Acc.
, vol.128
, pp. 3-16
-
-
Zhou, Y.1
|