-
1
-
-
0028815464
-
Protein structure prediction: Recognition of primary, secondary, and tertiary structural features from amino acid sequence
-
10.3109/10409239509085139 7587278
-
Protein structure prediction: recognition of primary, secondary, and tertiary structural features from amino acid sequence. Eisenhaber F, Crit Rev Biochem Mol Biol 1995 30 1 94 10.3109/10409239509085139 7587278
-
(1995)
Crit Rev Biochem Mol Biol
, vol.30
, pp. 1-94
-
-
Eisenhaber, F.1
-
2
-
-
0002740693
-
Protein structure prediction in 1D, 2D, and 3D
-
Protein structure prediction in 1D, 2D, and 3D. Rost B, Encyclopaedia Comput Chem 1998 3 2242 2255
-
(1998)
Encyclopaedia Comput Chem
, vol.3
, pp. 2242-2255
-
-
Rost, B.1
-
3
-
-
34249824268
-
Computational methods in protein structure prediction
-
DOI 10.1002/bit.21411
-
Computational methods in protein structure prediction. Floudas C, Biotechnol Bioeng 2007 97 207 213 10.1002/bit.21411 17455371 (Pubitemid 46852917)
-
(2007)
Biotechnology and Bioengineering
, vol.97
, Issue.2
, pp. 207-213
-
-
Floudas, C.A.1
-
4
-
-
0142210248
-
A computational pipeline for protein structure prediction and analysis at genome scale
-
DOI 10.1093/bioinformatics/btg262
-
A computational pipeline for protein structure prediction and analysis at genome scale. Shah M, Bioinformatics 2003 19 1985 10.1093/bioinformatics/btg262 14555633 (Pubitemid 37322344)
-
(2003)
Bioinformatics
, vol.19
, Issue.15
, pp. 1985-1996
-
-
Shah, M.1
Passovets, S.2
Kim, D.3
Ellrott, K.4
Wang, L.5
Vokler, I.6
LoCascio, P.7
Xu, D.8
Xu, Y.9
-
5
-
-
38749108825
-
Structural genomics: From genes to structures with valuable materials and many questions in between
-
DOI 10.1038/nmeth0208-129, PII NMETH0208-129
-
Structural genomics: from genes to structures with valuable materials and many questions in between. Fox BG, Nat Methods 2008 5 129 132 10.1038/nmeth0208-129 18235432 (Pubitemid 351181737)
-
(2008)
Nature Methods
, vol.5
, Issue.2
, pp. 129-132
-
-
Fox, B.G.1
Goulding, C.2
Malkowski, M.G.3
Stewart, L.4
Deacon, A.5
-
6
-
-
0028818340
-
Protein structure prediction by threading methods: Evaluation of current techniques
-
10.1002/prot.340230308 8710827
-
Protein structure prediction by threading methods: evaluation of current techniques. Lemer CMR, Proteins 1995 23 337 355 10.1002/prot.340230308 8710827
-
(1995)
Proteins
, vol.23
, pp. 337-355
-
-
Lemer, C.M.R.1
-
7
-
-
84995046262
-
A large-scale experiment to assess protein structure prediction methods
-
10.1002/prot.340230303 8710822
-
A large-scale experiment to assess protein structure prediction methods. Moult J, Proteins 1995 23 i iv 10.1002/prot.340230303 8710822
-
(1995)
Proteins
, vol.23
-
-
Moult, J.1
-
8
-
-
84864516302
-
Prediction of protein structure through evolution
-
Prediction of protein structure through evolution. Rost B, Handbook Chemoinformatics 2003 1789 1811
-
(2003)
Handbook Chemoinformatics
, pp. 1789-1811
-
-
Rost, B.1
-
9
-
-
77951941264
-
MULTICOM: A multi-level combination approach to protein structure prediction and its assessments in CASP8
-
10.1093/bioinformatics/btq058 20150411
-
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Wang Z, Bioinformatics 2010 26 882 888 10.1093/bioinformatics/btq058 20150411
-
(2010)
Bioinformatics
, vol.26
, pp. 882-888
-
-
Wang, Z.1
-
10
-
-
0017411710
-
The protein data bank: A computer based archival file for macromolecular structures
-
The protein data bank: a computer-based archival file for macromolecular structures*. Bernstein FC, J Mol Biol 1977 112 535 542 10.1016/S0022-2836(77)80200-3 875032 (Pubitemid 8109216)
-
(1977)
Journal of Molecular Biology
, vol.112
, Issue.3
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
-
11
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
10.1002/bip.360221211 6667333
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers 1983 22 2577 2637 10.1002/bip.360221211 6667333
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
12
-
-
78651277458
-
A series of PDB related databases for everyday needs
-
10.1093/nar/gkq1105 21071423
-
A series of PDB related databases for everyday needs. Joosten RP, Nucleic Acids Res 2011 39 411 D419 10.1093/nar/gkq1105 21071423
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Joosten, R.P.1
-
13
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul SF, Nucleic Acids Res 1997 25 3389 3402 10.1093/nar/25.17. 3389 9254694 (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
14
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
DOI 10.1093/nar/gki408
-
The HHpred interactive server for protein homology detection and structure prediction. Soding J, Nucleic Acids Res 2005 33 244 W248 10.1093/nar/gki408 15980461 (Pubitemid 44529917)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Soding, J.1
Biegert, A.2
Lupas, A.N.3
-
15
-
-
0037423702
-
COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
-
DOI 10.1016/S0022-2836(02)01371-2
-
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. Sadreyev R, Grishin N, J Mol Biol 2003 326 317 336 10.1016/S0022-2836(02)01371-2 12547212 (Pubitemid 36279378)
-
(2003)
Journal of Molecular Biology
, vol.326
, Issue.1
, pp. 317-336
-
-
Sadreyev, R.1
Grishin, N.2
-
16
-
-
84874934269
-
-
Available: http://supfam.org/PRC/
-
PRC, the profile comparer Available: http://supfam.org/PRC/
-
PRC, the Profile Comparer
-
-
-
18
-
-
79959931985
-
HMMER web server: Interactive sequence similarity searching
-
10.1093/nar/gkr367 21593126
-
HMMER web server: interactive sequence similarity searching. Finn RD, Nucleic Acids Res 2011 39 29 W37 10.1093/nar/gkr367 21593126
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Finn, R.D.1
-
19
-
-
23144465987
-
SCRATCH: A protein structure and structural feature prediction server
-
DOI 10.1093/nar/gki396
-
SCRATCH: a protein structure and structural feature prediction server. Cheng J, Nucleic Acids Res 2005 33 72 W76 10.1093/nar/gki396 15980571 (Pubitemid 44529882)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Cheng, J.1
Randall, A.Z.2
Sweredoski, M.J.3
Baldi, P.4
-
20
-
-
0034044314
-
The PSIPRED protein structure prediction server
-
10.1093/bioinformatics/16.4.404 10869041
-
The PSIPRED protein structure prediction server. McGuffin L, Bioinformatics 2000 16 404 10.1093/bioinformatics/16.4.404 10869041
-
(2000)
Bioinformatics
, vol.16
, pp. 404
-
-
McGuffin, L.1
-
21
-
-
0025183708
-
Basic local alignment search tool
-
2231712
-
Basic local alignment search tool. Altschul S, J Mol Biol 1990 215 403 410 2231712
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.1
-
22
-
-
62649147821
-
Sequence context-specific profiles for homology searching
-
10.1073/pnas.0810767106 19234132
-
Sequence context-specific profiles for homology searching. Biegert A, Söding J, Proc Natl Acad Sci 2009 106 3770 3775 10.1073/pnas.0810767106 19234132
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 3770-3775
-
-
Biegert, A.1
Söding, J.2
-
23
-
-
42149153292
-
A multi-template combination algorithm for protein comparative modeling
-
DOI 10.1186/1472-6807-8-18
-
A multi-template combination algorithm for protein comparative modeling. Cheng J, BMC Struct Biol 2008 8 18 10.1186/1472-6807-8-18 18366648 (Pubitemid 351537916)
-
(2008)
BMC Structural Biology
, vol.8
, pp. 18
-
-
Cheng, J.1
-
24
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
DOI 10.1093/nar/gki524
-
TM-align: a protein structure alignment algorithm based on the TM-score. Zhang Y, Skolnick J, Nucleic Acids Res 2005 33 2302 2309 10.1093/nar/gki524 15849316 (Pubitemid 41439897)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.7
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
25
-
-
0042622381
-
LGA: A method for finding 3D similarities in protein structures
-
DOI 10.1093/nar/gkg571
-
LGA: a method for finding 3D similarities in protein structures. Zemla A, Nucleic Acids Res 2003 31 3370 3374 10.1093/nar/gkg571 12824330 (Pubitemid 37442162)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3370-3374
-
-
Zemla, A.1
-
26
-
-
24644512819
-
SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures
-
DOI 10.1093/bioinformatics/bti582
-
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Zhou H, Zhou Y, Bioinformatics 2005 21 3615 3621 10.1093/bioinformatics/bti582 16020471 (Pubitemid 41264096)
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3615-3621
-
-
Zhou, H.1
Zhou, Y.2
-
27
-
-
0347383758
-
MODELLER: Generation and refinement of homology-based protein structure models
-
DOI 10.1016/S0076-6879(03)74020-8
-
Modeller: generation and refinement of homology-based protein structure models. Fiser A, Sali A, Methods Enzymol 2003 374 461 491 14696385 (Pubitemid 37531821)
-
(2003)
Methods in Enzymology
, vol.374
, pp. 461-491
-
-
Fiser, A.1
Sali, A.2
-
28
-
-
84891725544
-
Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9
-
Recursive protein modeling: a divide and conquer strategy for protein structure prediction and its case study in CASP9. Cheng J, J Bioinform Comput Biol 2011 10 3
-
(2011)
J Bioinform Comput Biol
, vol.10
, pp. 3
-
-
Cheng, J.1
-
29
-
-
78650905964
-
ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
-
21187238
-
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Leaver-Fay A, Methods Enzymol 2011 487 545 574 21187238
-
(2011)
Methods Enzymol
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
-
30
-
-
42449093288
-
Estimating quality of template-based protein models by alignment stability
-
DOI 10.1002/prot.21819
-
Estimating quality of template-based protein models by alignment stability. Chen H, Kihara D, Proteins 2008 71 1255 1274 18041762 (Pubitemid 351564051)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.71
, Issue.3
, pp. 1255-1274
-
-
Chen, H.1
Kihara, D.2
-
32
-
-
62849113729
-
SELECTpro: Effective protein model selection using a structure-based energy function resistant to BLUNDERs
-
10.1186/1472-6807-8-52 19055744
-
SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. Randall A, Baldi P, BMC Struct Biol 2008 8 52 10.1186/1472-6807-8-52 19055744
-
(2008)
BMC Struct Biol
, vol.8
, pp. 52
-
-
Randall, A.1
Baldi, P.2
-
34
-
-
42449119311
-
Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential
-
10.1002/prot.21813
-
Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential. Zhou H, Skolnick J, Proteins 2007 71 1211 1218 10.1002/prot.21813
-
(2007)
Proteins
, vol.71
, pp. 1211-1218
-
-
Zhou, H.1
Skolnick, J.2
-
35
-
-
66149156968
-
Evaluating the absolute quality of a single protein model using structural features and support vector machines
-
10.1002/prot.22275 19004001
-
Evaluating the absolute quality of a single protein model using structural features and support vector machines. Wang Z, Proteins 2009 75 638 647 10.1002/prot.22275 19004001
-
(2009)
Proteins
, vol.75
, pp. 638-647
-
-
Wang, Z.1
-
36
-
-
84891730221
-
Protein Tertiary Model Assessment Using Granular Machine Learning Techniques
-
Protein Tertiary Model Assessment Using Granular Machine Learning Techniques. Chida AA, Comp Sci Dissert 2012 65
-
(2012)
Comp Sci Dissert
, vol.65
-
-
Chida, A.A.1
-
37
-
-
79952673719
-
A machine learning-based method for protein global model quality assessment
-
10.1080/03081079.2010.544869
-
A machine learning-based method for protein global model quality assessment. Dong Q, Int J Gen 2011 40 417 425 10.1080/03081079.2010.544869
-
(2011)
Int J Gen
, vol.40
, pp. 417-425
-
-
Dong, Q.1
-
38
-
-
0037406141
-
Can correct protein models be identified?
-
Can correct protein models be identified? Wallner B, Elofsson A, Protein Sci 2009 12 1073 1086
-
(2009)
Protein Sci
, vol.12
, pp. 1073-1086
-
-
Wallner, B.1
Elofsson, A.2
-
39
-
-
80855128723
-
MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction
-
10.1002/prot.23185 21997748
-
MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction. Wang Q, Proteins 2011 79 185 195 10.1002/prot.23185 21997748
-
(2011)
Proteins
, vol.79
, pp. 185-195
-
-
Wang, Q.1
-
40
-
-
80855150026
-
Fast geometric consensus approach for protein model quality assessment
-
10.1089/cmb.2010.0170 21244273
-
Fast geometric consensus approach for protein model quality assessment. Adamczak R, J Comput Biol 2011 18 1807 1818 10.1089/cmb.2010.0170 21244273
-
(2011)
J Comput Biol
, vol.18
, pp. 1807-1818
-
-
Adamczak, R.1
-
41
-
-
0038386050
-
3D-Jury: A simple approach to improve protein structure predictions
-
DOI 10.1093/bioinformatics/btg124
-
3D-Jury: a simple approach to improve protein structure predictions. Ginalski K, Bioinformatics 2003 19 1015 1018 10.1093/bioinformatics/btg124 12761065 (Pubitemid 36675823)
-
(2003)
Bioinformatics
, vol.19
, Issue.8
, pp. 1015-1018
-
-
Ginalski, K.1
Elofsson, A.2
Fischer, D.3
Rychlewski, L.4
-
42
-
-
28444454499
-
Pcons5: Combining consensus, structural evaluation and fold recognition scores
-
DOI 10.1093/bioinformatics/bti702
-
Pcons5: combining consensus, structural evaluation and fold recognition scores. Wallner B, Elofsson A, Bioinformatics 2005 21 4248 4254 10.1093/bioinformatics/bti702 16204344 (Pubitemid 41724304)
-
(2005)
Bioinformatics
, vol.21
, Issue.23
, pp. 4248-4254
-
-
Wallner, B.1
Elofsson, A.2
-
43
-
-
34249753618
-
Support-vector networks
-
Support-vector networks. Cortes C, Vapnik V, Mach Learn 1995 20 273 297
-
(1995)
Mach Learn
, vol.20
, pp. 273-297
-
-
Cortes, C.1
Vapnik, V.2
-
44
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
DOI 10.1002/prot.20264
-
Scoring function for automated assessment of protein structure template quality. Zhang Y, Skolnick J, Proteins 2004 57 702 710 10.1002/prot.20264 15476259 (Pubitemid 39626992)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.57
, Issue.4
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
45
-
-
79958078892
-
APOLLO: A quality assessment service for single and multiple protein models
-
10.1093/bioinformatics/btr268 21546397
-
APOLLO: a quality assessment service for single and multiple protein models. Wang Z, Bioinformatics 2011 27 1715 1716 10.1093/bioinformatics/btr268 21546397
-
(2011)
Bioinformatics
, vol.27
, pp. 1715-1716
-
-
Wang, Z.1
-
46
-
-
74249120024
-
Prediction of global and local quality of CASP8 models by MULTICOM series
-
19544564
-
Prediction of global and local quality of CASP8 models by MULTICOM series. Cheng J, Proteins 2009 77 181 184 19544564
-
(2009)
Proteins
, vol.77
, pp. 181-184
-
-
Cheng, J.1
-
47
-
-
67849110005
-
NNcon: Improved protein contact map prediction using 2D-recursive neural networks
-
10.1093/nar/gkp305 19420062
-
NNcon: improved protein contact map prediction using 2D-recursive neural networks. Tegge AN, Nucleic Acids Res 2009 37 515 W518 10.1093/nar/gkp305 19420062
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Tegge, A.N.1
-
48
-
-
84860507958
-
Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms
-
DOI 10.1093/bioinformatics/bti1004
-
Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms. Cheng J, Baldi P, Bioinformatics 2005 21 75 i84 10.1093/bioinformatics/bti1004 15961501 (Pubitemid 41794477)
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Cheng, J.1
Baldi, P.2
-
49
-
-
80855132435
-
CASP9 target classification
-
10.1002/prot.23190 21997778
-
CASP9 target classification. Kinch LN, Proteins 2011 79 21 36 10.1002/prot.23190 21997778
-
(2011)
Proteins
, vol.79
, pp. 21-36
-
-
Kinch, L.N.1
-
50
-
-
75149164436
-
PreDisorder: Ab initio sequence-based prediction of protein disordered regions
-
10.1186/1471-2105-10-436
-
PreDisorder: ab initio sequence-based prediction of protein disordered regions. Deng X, BMC Bioinforma 2009 10 436 10.1186/1471-2105-10-436
-
(2009)
BMC Bioinforma
, vol.10
, pp. 436
-
-
Deng, X.1
|