-
1
-
-
0028815464
-
Protein structure prediction: Recognition of primary, secondary, and tertiary structural features from amino acid sequence
-
Eisenhaber, F., Persson, B., & Argos, P. Protein structure prediction: recognition of primary, secondary, and tertiary structural features from amino acid sequence. Crit. Rev. Biochem. Mol. Biol. 30, 1-94 (1995
-
(1995)
Crit. Rev. Biochem. Mol. Biol
, vol.30
, pp. 1-94
-
-
Eisenhaber, F.1
Persson, B.2
Argos, P.3
-
3
-
-
34249824268
-
Computational methods in protein structure prediction
-
Floudas, C. Computational methods in protein structure prediction. Biotechnol. Bioeng. 97, 207-213 (2007
-
(2007)
Biotechnol. Bioeng
, vol.97
, pp. 207-213
-
-
Floudas, C.1
-
4
-
-
0034780030
-
Pcons: A neural-network-based consensus predictor that improves fold recognition
-
Lundstrom, J., Rychlewski, L., Bujnicki, J., & Elofsson, A. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci. 10, 2354-2362 (2001
-
(2001)
Protein Sci
, vol.10
, pp. 2354-2362
-
-
Lundstrom, J.1
Rychlewski, L.2
Bujnicki, J.3
Elofsson, A.4
-
5
-
-
0242299169
-
Automatic consensus-based fold recognition using Pcons ProQ, and Pmodeller
-
Wallner, B., Fang, H., & Elofsson, A. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins: Struct. Funct. Bioinform. 53, 534-541 (2003
-
(2003)
Proteins: Struct. Funct. Bioinform
, vol.53
, pp. 534-541
-
-
Wallner, B.1
Fang, H.2
Elofsson, A.3
-
6
-
-
84864448769
-
Template-based protein structure modeling using the RaptorX web server
-
Kallberg, M., et al. Template-based protein structure modeling using the RaptorX web server. Nat. Protoc. 7, 1511-1522 (2012
-
(2012)
Nat. Protoc
, vol.7
, pp. 1511-1522
-
-
Kallberg, M.1
-
7
-
-
39149099199
-
The ModFOLD server for the quality assessment of protein structural models
-
McGuffin, L. J. The ModFOLD server for the quality assessment of protein structural models. Bioinformatics 24, 586-587 (2008
-
(2008)
Bioinformatics
, vol.24
, pp. 586-587
-
-
McGuffin, L.J.1
-
8
-
-
11344292852
-
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
-
Zhou, H., & Zhou, Y. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins: Struct. Funct. Bioinform. 58, 321-328 (2005
-
(2005)
Proteins: Struct. Funct. Bioinform
, vol.58
, pp. 321-328
-
-
Zhou, H.1
Zhou, Y.2
-
9
-
-
0033537993
-
Genthreader: An efficient and reliable protein fold recognition method for genomic sequences
-
Jones, D. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815 (1999
-
(1999)
J. Mol. Biol
, vol.287
, pp. 797-815
-
-
Jones, D.1
-
10
-
-
77954065271
-
I-TASSER: A unified platform for automated protein structure and function prediction
-
Roy, A., Kucukural, A., & Zhang, Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 5, 725-738 (2010
-
(2010)
Nat. Protoc
, vol.5
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
11
-
-
84907875010
-
The MULTICOM protein tertiary structure prediction system
-
Li, J., et al. The MULTICOM protein tertiary structure prediction system. Methods Mol. Biol. 1137, 29-41 (2014
-
(2014)
Methods Mol. Biol
, vol.1137
, pp. 29-41
-
-
Li, J.1
-
12
-
-
79955715769
-
A multiple-Template approach to protein threading
-
Peng, J., & Xu, J. A multiple-Template approach to protein threading. Proteins: Struct. Funct. Bioinform. 79, 1930-1939 (2011
-
(2011)
Proteins: Struct. Funct. Bioinform
, vol.79
, pp. 1930-1939
-
-
Peng, J.1
Xu, J.2
-
13
-
-
84946015803
-
Automatic prediction of protein 3d structures by probabilistic multi-Template homology modeling
-
Meier, A., & Soding, J. Automatic Prediction of Protein 3D Structures by Probabilistic Multi-Template Homology Modeling. Plos Comp. Biol. 11, e1004343 (2015
-
(2015)
Plos Comp. Biol
, vol.11
, pp. e1004343
-
-
Meier, A.1
Soding, J.2
-
14
-
-
33749139123
-
Distill: A suite of web servers for the prediction of one-, two-And three-dimensional structural features of proteins
-
Bau, D., et al. Distill: a suite of web servers for the prediction of one-, two-And three-dimensional structural features of proteins. BMC Bioinformatics 7, 402 (2006
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 402
-
-
Bau, D.1
-
15
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons, K., Kooperberg, C., Huang, E., & Baker, D. 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
-
(1997)
J. Mol. Biol
, vol.268
, pp. 209-225
-
-
Simons, K.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
16
-
-
0031307019
-
Evaluation of comparative protein structure modeling by MODELLER-3
-
Sanchez, R., & Sali, A. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins: Struct. Funct. Genet. 29, 50-58 (1997
-
(1997)
Proteins: Struct. Funct. Genet
, vol.29
, pp. 50-58
-
-
Sanchez, R.1
Sali, A.2
-
17
-
-
30344454371
-
Comparative modeling in CASP6 using consensus approach to template selection, sequencestructure alignment, and structure assessment
-
Venclovas, Č., & Margelevičius, M. Comparative modeling in CASP6 using consensus approach to template selection, sequencestructure alignment, and structure assessment. Proteins: Struct. Funct. Bioinform. 61, 99-105 (2005
-
(2005)
Proteins: Struct. Funct. Bioinform
, vol.61
, pp. 99-105
-
-
Venclovas, Č.1
Margelevičius, M.2
-
18
-
-
44349091007
-
Using multiple templates to improve quality of homology models in automated homology modeling
-
Larsson, P., Wallner, B., Lindahl, E., & Elofsson, A. Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci. 17, 990-1002 (2008
-
(2008)
Protein Sci
, vol.17
, pp. 990-1002
-
-
Larsson, P.1
Wallner, B.2
Lindahl, E.3
Elofsson, A.4
-
19
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Šali, A., & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815 (1993
-
(1993)
J. Mol. Biol
, Issue.234
, pp. 779-815
-
-
Šali, A.1
Blundell, T.L.2
-
20
-
-
0347383758
-
Modeller: Generation and refinement of homology-based protein structure models
-
Fiser, A., & Sali, A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 374, 461-491 (2003
-
(2003)
Methods Enzymol
, vol.374
, pp. 461-491
-
-
Fiser, A.1
Sali, A.2
-
21
-
-
0042622380
-
Swiss-model: An automated protein homology-modeling server
-
Schwede, T., Kopp, J., Guex, N., & Peitsch, M. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31, 3381 (2003
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3381
-
-
Schwede, T.1
Kopp, J.2
Guex, N.3
Peitsch, M.4
-
22
-
-
0026754015
-
Accurate modeling of protein conformation by automatic segment matching
-
Levitt, M. Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226, 507-533 (1992
-
(1992)
J. Mol. Biol
, vol.226
, pp. 507-533
-
-
Levitt, M.1
-
23
-
-
10744220076
-
Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
-
Petrey, D., et al. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins: Struct. Funct. Bioinform. 53, 430-435 (2003
-
(2003)
Proteins: Struct. Funct. Bioinform
, vol.53
, pp. 430-435
-
-
Petrey, D.1
-
24
-
-
42149153292
-
A multi-Template combination algorithm for protein comparative modeling
-
Cheng, J. A multi-Template combination algorithm for protein comparative modeling. BMC Struct. Biol. 8, 18 (2008
-
(2008)
BMC Struct. Biol
, vol.8
, pp. 18
-
-
Cheng, J.1
-
25
-
-
78149453870
-
A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction
-
Zhang, J., & Zhang, Y. A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. Plos One 5, e15386 (2010
-
(2010)
Plos One
, vol.5
, pp. e15386
-
-
Zhang, J.1
Zhang, Y.2
-
26
-
-
0042622381
-
LGA: A method for finding 3D similarities in protein structures
-
Zemla, A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res. 31, 3370-3374 (2003
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
27
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang, Y., & Skolnick, J. Scoring function for automated assessment of protein structure template quality. Proteins: Struct. Funct. Bioinform. 57, 702-710 (2004
-
(2004)
Proteins: Struct. Funct. Bioinform
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
28
-
-
74249114654
-
Evaluation of template-based models in CASP8 with standard measures
-
Cozzetto, D., et al. Evaluation of template-based models in CASP8 with standard measures. Proteins: Struct. Funct. Bioinform. 77, 18-28 (2009
-
(2009)
Proteins: Struct. Funct. Bioinform
, vol.77
, pp. 18-28
-
-
Cozzetto, D.1
-
29
-
-
84892959896
-
Assessment of template-based protein structure predictions in CASP10
-
Huang, Y. J., Mao, B., Aramini, J. M., & Montelione, G. T. Assessment of template-based protein structure predictions in CASP10. Proteins: Struct. Funct. Bioinform. 82, 43-56 (2014
-
(2014)
Proteins: Struct. Funct. Bioinform
, vol.82
, pp. 43-56
-
-
Huang, Y.J.1
Mao, B.2
Aramini, J.M.3
Montelione, G.T.4
-
30
-
-
84874240142
-
Designing and benchmarking the multicom protein structure prediction system
-
Li, J., Deng, X., Eickholt, J., & Cheng, J. Designing and benchmarking the MULTICOM protein structure prediction system. BMC Struct. Biol. 13, 2 (2013
-
(2013)
BMC Struct. Biol
, vol.13
, pp. 2
-
-
Li, J.1
Deng, X.2
Eickholt, J.3
Cheng, J.4
-
31
-
-
84862182129
-
The multicom toolbox for protein structure prediction
-
Cheng, J., Li, J., Wang, Z., Eickholt, J., & Deng, X. The MULTICOM toolbox for protein structure prediction. BMC Bioinformatics 13, 65 (2012
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 65
-
-
Cheng, J.1
Li, J.2
Wang, Z.3
Eickholt, J.4
Deng, X.5
-
32
-
-
77951941264
-
MULTICOM: A multi-level combination approach to protein structure prediction and its assessments in CASP8
-
Wang, Z., Eickholt, J., & Cheng, J. MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics 26, 882-888 (2010
-
(2010)
Bioinformatics
, vol.26
, pp. 882-888
-
-
Wang, Z.1
Eickholt, J.2
Cheng, J.3
-
33
-
-
84934283825
-
An improved integration of template-based and template-free protein structure modeling methods and its assessment in CASP11
-
Li, J., Adhikari, B., & Cheng, J. An improved integration of template-based and template-free protein structure modeling methods and its assessment in CASP11. Protein Pept. Lett. 22, 586-593 (2015
-
(2015)
Protein Pept. Lett
, vol.22
, pp. 586-593
-
-
Li, J.1
Adhikari, B.2
Cheng, J.3
-
34
-
-
84931048213
-
Large-scale model quality assessment for improving protein tertiary structure prediction
-
Cao, R., Bhattacharya, D., Adhikari, B., Li, J., & Cheng, J. Large-scale model quality assessment for improving protein tertiary structure prediction. Bioinformatics 31, i116-i123 (2015
-
(2015)
Bioinformatics
, vol.31
, pp. i116-i123
-
-
Cao, R.1
Bhattacharya, D.2
Adhikari, B.3
Li, J.4
Cheng, J.5
-
35
-
-
84945117520
-
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11
-
Li, J., Cao, R., & Cheng, J. A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11. BMC Bioinformatics 16, 337 (2015
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 337
-
-
Li, J.1
Cao, R.2
Cheng, J.3
-
36
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Soding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951-960 (2005
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Soding, J.1
-
37
-
-
79959931985
-
HMMER web server: Interactive sequence similarity searching
-
Finn, R. D., Clements, J., & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29-W37 (2011
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W29-W37
-
-
Finn, R.D.1
Clements, J.2
Eddy, S.R.3
-
38
-
-
62649147821
-
Sequence context-specific profiles for homology searching
-
Biegert, A., & Soding, J. Sequence context-specific profiles for homology searching. Proc. Natl. Acad. Sci. USA. 106, 3770-3775 (2009
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 3770-3775
-
-
Biegert, A.1
Soding, J.2
-
39
-
-
84870267223
-
The generalization of studen's problem when several different population variances are involved
-
Welch, B. L. The generalization of studen's problem when several different population variances are involved. Biometrika 34, 28-35 (1947
-
(1947)
Biometrika
, vol.34
, pp. 28-35
-
-
Welch, B.L.1
-
40
-
-
74549178560
-
MolProbity: All-Atom structure validation for macromolecular crystallography
-
Chen, V. B., et al. MolProbity: all-Atom structure validation for macromolecular crystallography. Acta Crystallogr. D66, 12-21 (2010
-
(2010)
Acta Crystallogr
, vol.D66
, pp. 12-21
-
-
Chen, V.B.1
-
41
-
-
81255123286
-
Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization
-
Xu, D., & Zhang, Y. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys. J. 101, 2525-2534 (2011
-
(2011)
Biophys. J.
, vol.101
, pp. 2525-2534
-
-
Xu, D.1
Zhang, Y.2
-
45
-
-
26444479778
-
Optimization by simulated annealing
-
Kirkpatrick, S., Gelatt Jr, C. D., & Vecchi, M. P. Optimization by Simulated Annealing. Science 220, 671-680 (1983
-
(1983)
Science
, vol.220
, pp. 671-680
-
-
Kirkpatrick, S.1
Gelatt, C.D.2
Vecchi, M.P.3
-
46
-
-
0021819411
-
Thermodynamical approach to the Traveling Salesman Problem: An efficient simulation algorithm
-
Černy, V. Thermodynamical approach to the Traveling Salesman Problem: an efficient simulation algorithm. J. Optim. Theory Appl. 45, 41-51 (1985
-
(1985)
J. Optim. Theory Appl
, vol.45
, pp. 41-51
-
-
Černy, V.1
-
48
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S., & Henikoff, J. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. 89, 10915-10919 (1992
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.2
-
49
-
-
44449124693
-
Fast procedure for reconstruction of full-Atom protein models from reduced representations
-
Rotkiewicz, P., & Skolnick, J. Fast procedure for reconstruction of full-Atom protein models from reduced representations. J. Comput. Chem. 29, 1460-1465 (2008
-
(2008)
J. Comput. Chem
, vol.29
, pp. 1460-1465
-
-
Rotkiewicz, P.1
Skolnick, J.2
-
50
-
-
70450106216
-
Improved prediction of protein side-chain conformations with SCWRL4
-
Krivov, G. G., Shapovalov, M. V., & Dunbrack, R. L. Improved prediction of protein side-chain conformations with SCWRL4. Proteins: Struct. Funct. Bioinform. 77, 778-795 (2009
-
(2009)
Proteins: Struct. Funct. Bioinform
, vol.77
, pp. 778-795
-
-
Krivov, G.G.1
Shapovalov, M.V.2
Dunbrack, R.L.3
|