-
1
-
-
12844260161
-
Comparative protein structure modeling and its applications to drug discovery
-
Jacobson M, Sali A. Comparative protein structure modeling and its applications to drug discovery. Annu Rep Med Chem. 2004;39(85):259-74.
-
(2004)
Annu Rep Med Chem
, vol.39
, Issue.85
, pp. 259-274
-
-
Jacobson, M.1
Sali, A.2
-
2
-
-
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 Bioinf. 2015;16(1):337.
-
(2015)
BMC Bioinf
, vol.16
, Issue.1
, pp. 337
-
-
Li, J.1
Cao, R.2
Cheng, J.3
-
3
-
-
84953341336
-
Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks
-
Cao R, Cheng J. Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks. Methods. 2016;93:84-91.
-
(2016)
Methods
, vol.93
, pp. 84-91
-
-
Cao, R.1
Cheng, J.2
-
4
-
-
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. 2015;31(12):i116-23.
-
(2015)
Bioinformatics
, vol.31
, Issue.12
, pp. 1116-1123
-
-
Cao, R.1
Bhattacharya, D.2
Adhikari, B.3
Li, J.4
Cheng, J.5
-
6
-
-
84907875010
-
The MULTICOM protein tertiary structure prediction system
-
Li J, Bhattacharya D, Cao R, Adhikari B, Deng X, Eickholt J, Cheng J. The MULTICOM protein tertiary structure prediction system. Protein Struct Prediction. 2014;1137:29-41.
-
(2014)
Protein Struct Prediction
, vol.1137
, pp. 29-41
-
-
Li, J.1
Bhattacharya, D.2
Cao, R.3
Adhikari, B.4
Deng, X.5
Eickholt, J.6
Cheng, J.7
-
8
-
-
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. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol. 1997;268(1):209-25.
-
(1997)
J Mol Biol
, vol.268
, Issue.1
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
9
-
-
0030203863
-
TreeView: an application to display phylogenetic trees on personal computer
-
Page R. TreeView: an application to display phylogenetic trees on personal computer. Comp Appl Biol Sci. 1996;12:357-8.
-
(1996)
Comp Appl Biol Sci
, vol.12
, pp. 357-358
-
-
Page, R.1
-
10
-
-
84962302439
-
FALCONat home: a high-throughput protein structure prediction server based on remote homologue recognition
-
Wang C, Zhang H, Zheng W-M, Xu D, Zhu J, Wang B, Ning K, Sun S, Li SC, Bu D. FALCON at home: a high-throughput protein structure prediction server based on remote homologue recognition. Bioinformatics. 2016;32(3):462-4.
-
(2016)
Bioinformatics
, vol.32
, Issue.3
, pp. 462-464
-
-
Wang, C.1
Zhang, H.2
Zheng, W.-M.3
Xu, D.4
Zhu, J.5
Wang, B.6
Ning, K.7
Sun, S.8
Li, S.C.9
Bu, D.10
-
11
-
-
55549086519
-
Fragment HMM: A new approach to protein structure prediction
-
Li SC, Bu D, Xu J, Li M. Fragment HMM: A new approach to protein structure prediction. Protein Sci. 2008;17(11):1925-34.
-
(2008)
Protein Sci
, vol.17
, Issue.11
, pp. 1925-1934
-
-
Li, S.C.1
Bu, D.2
Xu, J.3
Li, M.4
-
12
-
-
39449115394
-
I-TASSER server for protein 3D structure prediction
-
Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinf. 2008;9(1):40.
-
(2008)
BMC Bioinf
, vol.9
, Issue.1
, pp. 40
-
-
Zhang, Y.1
-
13
-
-
77951234057
-
MUFOLD: a new solution for protein 3D structure prediction
-
Zhang J, Wang Q, Barz B, He Z, Kosztin I, Shang Y, Xu D. MUFOLD: a new solution for protein 3D structure prediction. Proteins. 2010;78(5):1137-52.
-
(2010)
Proteins
, vol.78
, Issue.5
, pp. 1137-1152
-
-
Zhang, J.1
Wang, Q.2
Barz, B.3
He, Z.4
Kosztin, I.5
Shang, Y.6
Xu, D.7
-
14
-
-
80855147852
-
RaptorX: exploiting structure information for protein alignments by statistical inference
-
Peng J, Xu J. RaptorX: exploiting structure information for protein alignments by statistical inference. Proteins. 2011;79(S10):161-71.
-
(2011)
Proteins
, vol.79
, pp. 161-171
-
-
Peng, J.1
Xu, J.2
-
15
-
-
84966702489
-
A Stochastic Point Cloud Sampling Method for Multi-Template Protein Comparative Modeling
-
Li J, Cheng J. A Stochastic Point Cloud Sampling Method for Multi-Template Protein Comparative Modeling. Sci rep. 2016;6:25687.
-
(2016)
Sci rep
, vol.6
, pp. 25687
-
-
Li, J.1
Cheng, J.2
-
16
-
-
0345040873
-
Classification and regression by randomForest
-
Liaw A, Wiener M. Classification and regression by randomForest. R news. 2002;2(3):18-22.
-
(2002)
R news
, vol.2
, Issue.3
, pp. 18-22
-
-
Liaw, A.1
Wiener, M.2
-
17
-
-
84946763468
-
De novo protein conformational sampling using a probabilistic graphical model
-
Bhattacharya D, Cheng J. De novo protein conformational sampling using a probabilistic graphical model. Sci rep. 2015;5:16332.
-
(2015)
Sci rep
, vol.5
, pp. 16332
-
-
Bhattacharya, D.1
Cheng, J.2
-
18
-
-
84955127996
-
Benchmarking deep networks for predicting residue-specific quality of individual protein models in CASP11
-
Liu T, Wang Y, Eickholt J, Wang Z. Benchmarking deep networks for predicting residue-specific quality of individual protein models in CASP11. Sci Rep. 2016;6:19301.
-
(2016)
Sci Rep
, vol.6
, pp. 19301
-
-
Liu, T.1
Wang, Y.2
Eickholt, J.3
Wang, Z.4
-
19
-
-
84992217836
-
UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling
-
Bhattacharya D, Cao R, Cheng J. UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. Bioinformatics. 2016;32(18):2791-9. doi: 10.1093/bioinformatics/btw316.
-
(2016)
Bioinformatics
, vol.32
, Issue.18
, pp. 2791-2799
-
-
Bhattacharya, D.1
Cao, R.2
Cheng, J.3
-
20
-
-
84937727830
-
CONFOLD: residue-residue contact-guided ab initio protein folding
-
Adhikari B, Bhattacharya D, Cao R, Cheng J. CONFOLD: residue-residue contact-guided ab initio protein folding. Proteins: Struct Funct Bioinf. 2015;83(8):1436-49.
-
(2015)
Proteins: Struct Funct Bioinf
, vol.83
, Issue.8
, pp. 1436-1449
-
-
Adhikari, B.1
Bhattacharya, D.2
Cao, R.3
Cheng, J.4
-
22
-
-
39149099199
-
The ModFOLD server for the quality assessment of protein structural models
-
McGuffin L. The ModFOLD server for the quality assessment of protein structural models. Bioinformatics. 2008;24(4):586-7.
-
(2008)
Bioinformatics
, vol.24
, Issue.4
, pp. 586-587
-
-
McGuffin, L.1
-
23
-
-
80855128723
-
MUFOLD-WQA: a new selective consensus method for quality assessment in protein structure prediction
-
Wang Q, Vantasin K, Xu D, Shang Y. MUFOLD-WQA: a new selective consensus method for quality assessment in protein structure prediction. Proteins. 2011;79(SupplementS10):185-95.
-
(2011)
Proteins
, vol.79
, pp. 185-195
-
-
Wang, Q.1
Vantasin, K.2
Xu, D.3
Shang, Y.4
-
24
-
-
77950478720
-
Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments
-
McGuffin L, Roche D. Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics. 2010;26(2):182-8.
-
(2010)
Bioinformatics
, vol.26
, Issue.2
, pp. 182-188
-
-
McGuffin, L.1
Roche, D.2
-
25
-
-
84946236899
-
Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11
-
Cao R, Bhattacharya D, Adhikari B, Li J, Cheng J. Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11. Proteins: Structure, Function, and Bioinformatics. 2015;84:247-59. doi: 10.1002/prot.24924.
-
(2015)
Proteins: Structure, Function, and Bioinformatics
, vol.84
, pp. 247-259
-
-
Cao, R.1
Bhattacharya, D.2
Adhikari, B.3
Li, J.4
Cheng, J.5
-
26
-
-
84960155202
-
Methods of model accuracy estimation can help selecting the best models from decoy sets: assessment of model accuracy estimations in CASP11
-
Kryshtafovych A, Barbato A, Monastyrskyy B, Fidelis K, Schwede T, Tramontano A. Methods of model accuracy estimation can help selecting the best models from decoy sets: assessment of model accuracy estimations in CASP11. Proteins: Structure, Function, and Bioinformatics. 2015;84:349-69. doi: 10.1002/prot.24919.
-
(2015)
Proteins: Structure, Function, and Bioinformatics
, vol.84
, pp. 349-369
-
-
Kryshtafovych, A.1
Barbato, A.2
Monastyrskyy, B.3
Fidelis, K.4
Schwede, T.5
Tramontano, A.6
-
27
-
-
84899522371
-
Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment
-
Cao R, Wang Z, Cheng J. Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment. BMC Struct Biol. 2014;14(1):13.
-
(2014)
BMC Struct Biol
, vol.14
, Issue.1
, pp. 13
-
-
Cao, R.1
Wang, Z.2
Cheng, J.3
-
28
-
-
84899950974
-
SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines
-
Cao R, Wang Z, Wang Y, Cheng J. SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines. BMC Bioinf. 2014;15(1):120.
-
(2014)
BMC Bioinf
, vol.15
, Issue.1
, pp. 120
-
-
Cao, R.1
Wang, Z.2
Wang, Y.3
Cheng, J.4
-
29
-
-
34247281977
-
Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials
-
Rykunov D, Fiser A. Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials. Proteins: Struct Funct Bioinf. 2007;67(3):559-68.
-
(2007)
Proteins: Struct Funct Bioinf
, vol.67
, Issue.3
, pp. 559-568
-
-
Rykunov, D.1
Fiser, A.2
-
30
-
-
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. 2010;5(10):e15386.
-
(2010)
PLoS One
, vol.5
, Issue.10
-
-
Zhang, J.1
Zhang, Y.2
-
31
-
-
66149156968
-
Evaluating the absolute quality of a single protein model using structural features and support vector machines
-
Wang Z, Tegge AN, Cheng J. Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins. 2009;75(3):638-47.
-
(2009)
Proteins
, vol.75
, Issue.3
, pp. 638-647
-
-
Wang, Z.1
Tegge, A.N.2
Cheng, J.3
-
32
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
Shen M, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006;15(11):2507-24.
-
(2006)
Protein Sci
, vol.15
, Issue.11
, pp. 2507-2524
-
-
Shen, M.1
Sali, A.2
-
33
-
-
84962409085
-
Protein single-model quality assessment by feature-based probability density functions
-
Cao R, Cheng J. Protein single-model quality assessment by feature-based probability density functions. Sci Rep. 2016;6:23990.
-
(2016)
Sci Rep
, vol.6
, pp. 23990
-
-
Cao, R.1
Cheng, J.2
-
34
-
-
77952850689
-
Quality assessment of protein model-structures using evolutionary conservation
-
Kalman M, Ben-Tal N. Quality assessment of protein model-structures using evolutionary conservation. Bioinformatics. 2010;26(10):1299-307.
-
(2010)
Bioinformatics
, vol.26
, Issue.10
, pp. 1299-1307
-
-
Kalman, M.1
Ben-Tal, N.2
-
35
-
-
0026610767
-
Assessment of protein models with three-dimensional profiles
-
Liithy R, Bowie J, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992;356:83-5.
-
(1992)
Nature
, vol.356
, pp. 83-85
-
-
Liithy, R.1
Bowie, J.2
Eisenberg, D.3
-
36
-
-
84865844930
-
Improved model quality assessment using ProQ2
-
Ray A, Lindahl E, Wallner B. Improved model quality assessment using ProQ2. BMC Bioinf. 2012;13(1):224.
-
(2012)
BMC Bioinf
, vol.13
, Issue.1
, pp. 224
-
-
Ray, A.1
Lindahl, E.2
Wallner, B.3
-
37
-
-
84882263302
-
Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding
-
Mishra A, Rao S, Mittal A, Jayaram B. Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding. Biochim Biophys Acta Proteins Proteomics. 2013;1834(8):1520-31.
-
(2013)
Biochim Biophys Acta Proteins Proteomics
, vol.1834
, Issue.8
, pp. 1520-1531
-
-
Mishra, A.1
Rao, S.2
Mittal, A.3
Jayaram, B.4
-
38
-
-
79551613290
-
Toward the estimation of the absolute quality of individual protein structure models
-
Benkert P, Biasini M, Schwede T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics. 2011;27(3):343-50.
-
(2011)
Bioinformatics
, vol.27
, Issue.3
, pp. 343-350
-
-
Benkert, P.1
Biasini, M.2
Schwede, T.3
-
39
-
-
84907271392
-
Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms
-
Manavalan B, Lee J, Lee J. Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms. PLoS One. 2014;9(9):e106542.
-
(2014)
PLoS One
, vol.9
, Issue.9
-
-
Manavalan, B.1
Lee, J.2
Lee, J.3
-
40
-
-
84966349243
-
ProQ2: Estimation of Model Accuracy Implemented in Rosetta
-
Uziela K, Wallner B. ProQ2: Estimation of Model Accuracy Implemented in Rosetta. Bioinformatics. 2016;32(9):1411-3.
-
(2016)
Bioinformatics
, vol.32
, Issue.9
, pp. 1411-1413
-
-
Uziela, K.1
Wallner, B.2
-
41
-
-
85000509006
-
ProQ3: improved model quality assessments using Rosetta energy terms\
-
arXiv preprint arXiv:160205832
-
Uziela K, Wallner B, Elofsson A. ProQ3: improved model quality assessments using Rosetta energy terms. 2016. arXiv preprint arXiv:160205832.
-
(2016)
-
-
Uziela, K.1
Wallner, B.2
Elofsson, A.3
-
42
-
-
84959329050
-
ResQ: an approach to unified estimation of B-factor and residue-specific error in protein structure prediction
-
Yang J, Wang Y, Zhang Y. ResQ: an approach to unified estimation of B-factor and residue-specific error in protein structure prediction. J Mol Biol. 2016;428(4):693-701.
-
(2016)
J Mol Biol
, vol.428
, Issue.4
, pp. 693-701
-
-
Yang, J.1
Wang, Y.2
Zhang, Y.3
-
44
-
-
84906486716
-
Generic object detection with dense neural patterns and regionlets
-
arXiv preprint arXiv:14044316.
-
Zou WY, Wang X, Sun M, Lin Y. Generic object detection with dense neural patterns and regionlets. 2014. arXiv preprint arXiv:14044316.
-
(2014)
-
-
Zou, W.Y.1
Wang, X.2
Sun, M.3
Lin, Y.4
-
45
-
-
84963949906
-
Mastering the game of Go with deep neural networks and tree search
-
Silver D, Huang A, Maddison CJ, Guez A, Sifre L, van den Driessche G, Schrittwieser J, Antonoglou I, Panneershelvam V, Lanctot M. Mastering the game of Go with deep neural networks and tree search. Nature. 2016;529(7587):484-9.
-
(2016)
Nature
, vol.529
, Issue.7587
, pp. 484-489
-
-
Silver, D.1
Huang, A.2
Maddison, C.J.3
Guez, A.4
Sifre, L.5
Driessche, G.6
Schrittwieser, J.7
Antonoglou, I.8
Panneershelvam, V.9
Lanctot, M.10
-
46
-
-
84870415234
-
Predicting protein residue-residue contacts using deep networks and boosting
-
Eickholt J, Cheng J. Predicting protein residue-residue contacts using deep networks and boosting. Bioinformatics. 2012;28(23):3066-72.
-
(2012)
Bioinformatics
, vol.28
, Issue.23
, pp. 3066-3072
-
-
Eickholt, J.1
Cheng, J.2
-
47
-
-
84962320188
-
3DRobot: automated generation of diverse and well-packed protein structure decoys
-
Deng H, Jia Y, Zhang Y. 3DRobot: automated generation of diverse and well-packed protein structure decoys. Bioinformatics. 2016;32(3):378-87.
-
(2016)
Bioinformatics
, vol.32
, Issue.3
, pp. 378-387
-
-
Deng, H.1
Jia, Y.2
Zhang, Y.3
-
48
-
-
0043180474
-
PISCES: a protein sequence culling server
-
Wang G, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics. 2003;19(12):1589-91.
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack, R.L.2
-
49
-
-
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. 1997;268(1):209-25.
-
(1997)
J Mol Biol
, vol.268
, Issue.1
, pp. 209-225
-
-
Simons, K.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
50
-
-
0141978673
-
Comparative protein structure modeling by iterative alignment, model building and model assessment
-
John B, Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res. 2003;31(14):3982-92.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.14
, pp. 3982-3992
-
-
John, B.1
Sali, A.2
-
51
-
-
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 Bioinf. 2004;57(4):702-10.
-
(2004)
Proteins: Struct Funct Bioinf
, vol.57
, Issue.4
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
52
-
-
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. 2003;31(13):3370-4.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3370-3374
-
-
Zemla, A.1
-
53
-
-
80054694711
-
GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction
-
Zhou H, Skolnick J. GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J. 2011;101(8):2043-52.
-
(2011)
Biophys J
, vol.101
, Issue.8
, pp. 2043-2052
-
-
Zhou, H.1
Skolnick, J.2
-
54
-
-
34250829219
-
OPUS-Ca: a knowledge-based potential function requiring only Cα positions
-
Wu Y, Lu M, Chen M, Li J, Ma J. OPUS-Ca: a knowledge-based potential function requiring only Cα positions. Protein Sci. 2007;16(7):1449-63.
-
(2007)
Protein Sci
, vol.16
, Issue.7
, pp. 1449-1463
-
-
Wu, Y.1
Lu, M.2
Chen, M.3
Li, J.4
Ma, J.5
-
55
-
-
46449132707
-
Specific interactions for ab initio folding of protein terminal regions with secondary structures
-
Yang Y, Zhou Y. Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins: Struct Funct Bioinf. 2008;72(2):793-803.
-
(2008)
Proteins: Struct Funct Bioinf
, vol.72
, Issue.2
, pp. 793-803
-
-
Yang, Y.1
Zhou, Y.2
-
56
-
-
0013344078
-
Training products of experts by minimizing contrastive divergence
-
Hinton GE. Training products of experts by minimizing contrastive divergence. Neural Comput. 2002;14(8):1771-800.
-
(2002)
Neural Comput
, vol.14
, Issue.8
, pp. 1771-1800
-
-
Hinton, G.E.1
-
57
-
-
34547521683
-
An improved learning algorithm based on the Broyden-Fletcher-Goldfarb-Shanno (BFGS) method for back propagation neural networks
-
IEEE.IEEE Computer SocietyWashington, DC, USA.
-
Nawi NM, Ransing MR, Ransing RS: An improved learning algorithm based on the Broyden-Fletcher-Goldfarb-Shanno (BFGS) method for back propagation neural networks.In Sixth International Conference on Intelligent Systems Design and Applications(Vol. 1, pp. 152-157). IEEE.ISBN:0-7695-2528-8.IEEE Computer SocietyWashington, DC, USA.
-
In Sixth International Conference on Intelligent Systems Design and Applications
, vol.1
, pp. 152-157
-
-
Nawi, N.M.1
Ransing, M.R.2
Ransing, R.S3
-
58
-
-
76749092270
-
The WEKA data mining software: an update
-
Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten IH. The WEKA data mining software: an update. ACM SIGKDD Explor Newsl. 2009;11(1):10-8.
-
(2009)
ACM SIGKDD Explor Newsl
, vol.11
, Issue.1
, pp. 10-18
-
-
Hall, M.1
Frank, E.2
Holmes, G.3
Pfahringer, B.4
Reutemann, P.5
Witten, I.H.6
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