-
1
-
-
33846200437
-
Prediction-based fingerprints of protein-protein interactions
-
A. Porollo and J. Meller, "Prediction-based fingerprints of protein-protein interactions, " Proteins: Structure, Function and Genetics, vol. 66, no. 3, pp. 630-645, 2007.
-
(2007)
Proteins: Structure, Function and Genetics
, vol.66
, Issue.3
, pp. 630-645
-
-
Porollo, A.1
Meller, J.2
-
2
-
-
0035342450
-
Residue frequencies and pairing preferences at protein-protein interfaces
-
F. Glaser, D. M. Steinberg, I. A. Vakser, and N. Ben-Tal, "Residue frequencies and pairing preferences at protein-protein interfaces, " Proteins, vol. 43, no. 2, pp. 89-102, 2001.
-
(2001)
Proteins
, vol.43
, Issue.2
, pp. 89-102
-
-
Glaser, F.1
Steinberg, D.M.2
Vakser, I.A.3
Ben-Tal, N.4
-
3
-
-
0036469060
-
Unraveling hot spots in binding interfaces: Progress and challenges
-
W. L. DeLano, "Unraveling hot spots in binding interfaces: progress and challenges, " Current Opinion in Structural Biology, vol. 12, no. 1, pp. 14-20, 2002.
-
(2002)
Current Opinion in Structural Biology
, vol.12
, Issue.1
, pp. 14-20
-
-
DeLano, W.L.1
-
4
-
-
0035882570
-
Prediction of protein interaction sites from sequence profile and residue neighbor list
-
H. Zhou and Y. Shan, "Prediction of protein interaction sites from sequence profile and residue neighbor list, " Proteins: Structure, Function and Genetics, vol. 44, no. 3, pp. 336-343, 2001.
-
(2001)
Proteins: Structure, Function and Genetics
, vol.44
, Issue.3
, pp. 336-343
-
-
Zhou, H.1
Shan, Y.2
-
5
-
-
0036681416
-
Scoring residue conservation
-
W. S. J. Valdar, "Scoring residue conservation, " Proteins: Structure, Function and Genetics, vol. 48, no. 2, pp. 227-241, 2002.
-
(2002)
Proteins: Structure, Function and Genetics
, vol.48
, Issue.2
, pp. 227-241
-
-
Valdar, W.S.J.1
-
6
-
-
24344484686
-
Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data
-
H. Chen and H. X. Zhou, "Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data, " Proteins: Structure, Function and Genetics, vol. 61, no. 1, pp. 21-35, 2005.
-
(2005)
Proteins: Structure, Function and Genetics
, vol.61
, Issue.1
, pp. 21-35
-
-
Chen, H.1
Zhou, H.X.2
-
7
-
-
1842765629
-
Prediction of protein-protein interaction sites using support vector machines
-
A. Koike and T. Takagi, "Prediction of protein-protein interaction sites using support vector machines, " Protein Engineering, Design and Selection, vol. 17, no. 2, pp. 165-173, 2004.
-
(2004)
Protein Engineering, Design and Selection
, vol.17
, Issue.2
, pp. 165-173
-
-
Koike, A.1
Takagi, T.2
-
8
-
-
30644470508
-
Predicting protein interaction sites from residue spatial sequence profile and evolution rate
-
B. Wang, P. Chen, D. Huang, J. Li, T. Lok, and M. R. Lyu, "Predicting protein interaction sites from residue spatial sequence profile and evolution rate, " FEBS Letters, vol. 580, no. 2, pp. 380-384, 2006.
-
(2006)
FEBS Letters
, vol.580
, Issue.2
, pp. 380-384
-
-
Wang, B.1
Chen, P.2
Huang, D.3
Li, J.4
Lok, T.5
Lyu, M.R.6
-
9
-
-
33748779553
-
Insights into protein-protein Interfaces using a Bayesian network predictionmethod
-
J. R. Bradford, C. J. Needham, A. J. Bulpitt, and D. R. Westhead, "Insights into protein-protein Interfaces using a Bayesian network predictionmethod, " Journal ofMolecular Biology, vol. 362, no. 2, pp. 365-386, 2006.
-
(2006)
Journal OfMolecular Biology
, vol.362
, Issue.2
, pp. 365-386
-
-
Bradford, J.R.1
Needham, C.J.2
Bulpitt, A.J.3
Westhead, D.R.4
-
10
-
-
33751353420
-
Modelling interaction sites in protein domains with interaction profile hidden Markov models
-
T. Friedrich, B. Pils, T. Dandekar, J. Schultz, and T. Muller, "Modelling interaction sites in protein domains with interaction profile hidden Markov models, " Bioinformatics, vol. 22, no. 23, pp. 2851-2857, 2006.
-
(2006)
Bioinformatics
, vol.22
, Issue.23
, pp. 2851-2857
-
-
Friedrich, T.1
Pils, B.2
Dandekar, T.3
Schultz, J.4
Muller, T.5
-
11
-
-
34548767667
-
Interaction-site prediction for protein complexes: A critical assessment
-
H. Zhou and S. Qin, "Interaction-site prediction for protein complexes: a critical assessment, " Bioinformatics, vol. 23, no. 17, pp. 2203-2209, 2007.
-
(2007)
Bioinformatics
, vol.23
, Issue.17
, pp. 2203-2209
-
-
Zhou, H.1
Qin, S.2
-
12
-
-
68749110968
-
Exploitingthree kinds of interface propensities to identify protein binding sites
-
B. Liu, X. Wang, L. Lin, Q. Dong, and X. Wang, "Exploitingthree kinds of interface propensities to identify protein binding sites, " Computational Biology andChemistry, vol. 33, no. 4, pp. 303-311, 2009.
-
(2009)
Computational Biology AndChemistry
, vol.33
, Issue.4
, pp. 303-311
-
-
Liu, B.1
Wang, X.2
Lin, L.3
Dong, Q.4
Wang, X.5
-
13
-
-
71549172792
-
Prediction of protein binding sites in protein structures using hiddenMarkov support vector machine
-
article 381
-
B. Liu, X. Wang, L. Lin, B. Tang, and Q. Dong, "Prediction of protein binding sites in protein structures using hiddenMarkov support vector machine, " BMC Bioinformatics, vol. 10, article 381, 2009.
-
(2009)
BMC Bioinformatics
, vol.10
-
-
Liu, B.1
Wang, X.2
Lin, L.3
Tang, B.4
Dong, Q.5
-
14
-
-
33644873706
-
The RCSB PDB information portal for structural genomics
-
A. Kouranov, L. Xie, J. de la Cruz et al., "The RCSB PDB information portal for structural genomics, " Nucleic Acids Research., vol. 34, pp. D302-D305, 2006.
-
(2006)
Nucleic Acids Research.
, vol.34
, pp. D302-D305
-
-
Kouranov, A.1
Xie, L.2
De La Cruz, J.3
-
15
-
-
1942421209
-
Hidden markov support vector machines
-
August
-
Y. Altun, I. Tsochantaridis, and T. Hofmann, "Hidden markov support vector machines, " in Proceedings of the 20th International Conference on Machine Learning (ICML 03), pp. 3-10, August 2003.
-
(2003)
Proceedings of the 20th International Conference on Machine Learning (ICML 03)
, pp. 3-10
-
-
Altun, Y.1
Tsochantaridis, I.2
Hofmann, T.3
-
16
-
-
70450152077
-
Protein remote homology detection using order profiles
-
Shanghai, China, August
-
B. Liu, L. Lin, and X. Wang, "Protein remote homology detection using order profiles, " in Proceedings of the International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS 09), pp. 255-260, Shanghai, China, August 2009.
-
(2009)
Proceedings of the International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS 09)
, pp. 255-260
-
-
Liu, B.1
Lin, L.2
Wang, X.3
-
17
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
W. Kabsch and C. Sander, "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, " Biopolymers, vol. 22, no. 12, pp. 2577-2637, 1983.
-
(1983)
Biopolymers
, vol.22
, Issue.12
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
18
-
-
84867004398
-
Using amino acid physicochemical distance transformation for fast protein remote homology detection
-
Article ID e46633
-
B. Liu, X. Wang, Q. Chen, Q. Dong, and X. Lan, "Using amino acid physicochemical distance transformation for fast protein remote homology detection, " PLoS ONE, vol. 7, no. 9, Article ID e46633, 2012.
-
(2012)
PLoS ONE
, vol.7
, Issue.9
-
-
Liu, B.1
Wang, X.2
Chen, Q.3
Dong, Q.4
Lan, X.5
-
19
-
-
58149345703
-
A discriminativemethod for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis
-
article 510
-
B. Liu, X. Wang, L. Lin, and Q. Dong, "A discriminativemethod for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis, " BMC Bioinformatics, vol. 9, article 510, 2008.
-
(2008)
BMC Bioinformatics
, vol.9
-
-
Liu, B.1
Wang, X.2
Lin, L.3
Dong, Q.4
-
20
-
-
84892972298
-
Proteinremote homology detection by combining Chous pseudo amino acid composition and profile-based protein representation
-
B. Liu, X. Wang, Q. Zou, Q. Dong, and Q. Chen, "Proteinremote homology detection by combining Chous pseudo amino acid composition and profile-based protein representation, " Molecular Informatics, vol. 32, no. 9-10, pp. 775-782, 2013.
-
(2013)
Molecular Informatics
, vol.32
, Issue.9-10
, pp. 775-782
-
-
Liu, B.1
Wang, X.2
Zou, Q.3
Dong, Q.4
Chen, Q.5
-
21
-
-
84901288109
-
Using distances between Top-n-gram and residue pairs for protein remote homology detection
-
B. Liu, J. Xu, Q. Zou et al., "Using distances between Top-n-gram and residue pairs for protein remote homology detection, "BMC Bioinformatics, vol. 15, supplement 2, p. S3, 2014.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. S3
-
-
Liu, B.1
Xu, J.2
Zou, Q.3
-
22
-
-
84892954329
-
Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection
-
B. Liu, "Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection, " Bioinformatics, vol. 30, no. 4, pp. 472-479, 2014.
-
(2014)
Bioinformatics
, vol.30
, Issue.4
, pp. 472-479
-
-
Liu, B.1
-
23
-
-
59149087824
-
Prediction of proteinprotein interaction sites in sequences and 3D structures by
-
random forests Article ID e1000278
-
M. Sikic, S. Tomic, and K. Vlahoviɥek, "Prediction of proteinprotein interaction sites in sequences and 3D structures by random forests, " PLoS Computational Biology, vol. 5, no. 1, Article ID e1000278, 2009.
-
(2009)
PLoS Computational Biology
, vol.5
, Issue.1
-
-
Sikic, M.1
Tomic, S.2
Vlahoviɥek, K.3
-
24
-
-
34047104592
-
Protein-protein interaction site prediction based on conditional random fields
-
M. H. Li, L. Lin, X. Wang, and T. Liu, "Protein-protein interaction site prediction based on conditional random fields, " Bioinformatics, vol. 23, no. 5, pp. 597-604, 2007.
-
(2007)
Bioinformatics
, vol.23
, Issue.5
, pp. 597-604
-
-
Li, M.H.1
Lin, L.2
Wang, X.3
Liu, T.4
-
25
-
-
84887196363
-
QChIPat: A quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions
-
B. Liu, "QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions, " BMC Genomics, vol. 14, supplement 8, p. S3, 2013.
-
(2013)
BMC Genomics
, vol.14
, pp. S3
-
-
Liu, B.1
-
26
-
-
84863432335
-
Prediction of ketoacyl synthase family using reduced amino acid alphabets
-
W. Chen, P. Feng, and H. Lin, "Prediction of ketoacyl synthase family using reduced amino acid alphabets, " Journal of IndustrialMicrobiology and Biotechnology, vol. 39, no. 4, pp. 579-584, 2012.
-
(2012)
Journal of IndustrialMicrobiology and Biotechnology
, vol.39
, Issue.4
, pp. 579-584
-
-
Chen, W.1
Feng, P.2
Lin, H.3
-
27
-
-
84885112194
-
AcalPred: A sequence-based tool for discriminating between acidic and alkaline enzymes
-
Article IDe75726
-
H. Lin, W. Chen, and H. Ding, "AcalPred: a sequence-based tool for discriminating between acidic and alkaline enzymes, " PLoS ONE, vol. 8, no. 10, Article IDe75726, 2013.
-
(2013)
PLoS ONE
, vol.8
, Issue.10
-
-
Lin, H.1
Chen, W.2
Ding, H.3
-
28
-
-
84898434605
-
DNA physical parameters modulate nucleosome positioning in the Saccharomyces cerevisiae genome
-
W. Chen, H. Lin, and P. M. Feng, "DNA physical parameters modulate nucleosome positioning in the Saccharomyces cerevisiae genome, " Current Bioinformatics, vol. 9, no. 2, pp. 188-193, 2014.
-
(2014)
Current Bioinformatics
, vol.9
, Issue.2
, pp. 188-193
-
-
Chen, W.1
Lin, H.2
Feng, P.M.3
-
29
-
-
84884269845
-
Identification of antioxidants from sequence information using Naive Bayes
-
Article ID 567529
-
P.-M. Feng, H. Lin, and W. Chen, "Identification of antioxidants from sequence information using Naive Bayes, " Computational and Mathematical Methods in Medicine, vol. 2013, Article ID 567529, 5 pages, 2013.
-
(2013)
Computational and Mathematical Methods in Medicine
, vol.2013
, pp. 5
-
-
Feng, P.-M.1
Lin, H.2
Chen, W.3
-
30
-
-
84870391329
-
Identification ofmycobacterialmembrane proteins and their types using overrepresented tripeptide compositions
-
C. Ding, L. Yuan, S. Guo, H. Lin, and W. Chen, "Identification ofmycobacterialmembrane proteins and their types using overrepresented tripeptide compositions, " Journal of Proteomics, vol. 77, pp. 321-328, 2012.
-
(2012)
Journal of Proteomics
, vol.77
, pp. 321-328
-
-
Ding, C.1
Yuan, L.2
Guo, S.3
Lin, H.4
Chen, W.5
-
31
-
-
84862831800
-
Identification of voltage-gated potassium channel subfamilies from sequence information using support vector machine
-
W. Chen and H. Lin, "Identification of voltage-gated potassium channel subfamilies from sequence information using support vector machine, " Computers in Biology andMedicine, vol. 42, no. 4, pp. 504-507, 2012.
-
(2012)
Computers in Biology AndMedicine
, vol.42
, Issue.4
, pp. 504-507
-
-
Chen, W.1
Lin, H.2
-
32
-
-
84885640993
-
IHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition
-
P. M. Feng, W. Chen, H. Lin, and K. Chou, "iHSP-PseRAAAC: identifying the heat shock protein families using pseudo reduced amino acid alphabet composition, "Analytical Biochemistry, vol. 442, no. 1, pp. 118-125, 2013.
-
(2013)
Analytical Biochemistry
, vol.442
, Issue.1
, pp. 118-125
-
-
Feng, P.M.1
Chen, W.2
Lin, H.3
Chou, K.4
-
33
-
-
84868128310
-
INuc-PhysChem: A sequence-based predictor for identifying nucleosomes via physicochemical properties
-
Article ID e47843
-
W. Chen, H. Lin, P. Feng, C. Ding, Y. Zuo, and K. Chou, "iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties, " PLoS ONE, vol. 7, no. 10, Article ID e47843, 2012.
-
(2012)
PLoS ONE
, vol.7
, Issue.10
-
-
Chen, W.1
Lin, H.2
Feng, P.3
Ding, C.4
Zuo, Y.5
Chou, K.6
-
34
-
-
84896463976
-
INuc-PseKNC: A sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition
-
S. H. Guo, E. Z. Deng, L. Q. Xu et al., "iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition, " Bioinformatics, vol. 30, no. 11, pp. 1522-1529, 2014.
-
(2014)
Bioinformatics
, vol.30
, Issue.11
, pp. 1522-1529
-
-
Guo, S.H.1
Deng, E.Z.2
Xu, L.Q.3
-
35
-
-
84876053736
-
IRSpot-PseDNC: Identify recombination spots with pseudo dinucleotide composition
-
W. Chen, P. Feng, H. Lin, and K. Chou, "IRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition, " Nucleic Acids Research, vol. 41, no. 6, p. e68, 2013.
-
(2013)
Nucleic Acids Research
, vol.41
, Issue.6
, pp. e68
-
-
Chen, W.1
Feng, P.2
Lin, H.3
Chou, K.4
-
36
-
-
84878657414
-
Naive bayes classifier with feature selection to identify phage virion proteins
-
Article ID 530696
-
P. Feng, H. Ding, W. Chen, and H. Lin, "Naive bayes classifier with feature selection to identify phage virion proteins, " Computational and Mathematical Methods in Medicine, vol. 2013, Article ID 530696, 6 pages, 2013.
-
(2013)
Computational and Mathematical Methods in Medicine
, vol.2013
, pp. 6
-
-
Feng, P.1
Ding, H.2
Chen, W.3
Lin, H.4
-
37
-
-
84876306464
-
Prediction of Golgi-resident protein types by using feature selection technique
-
H. Ding, S. Guo, E. Deng et al., "Prediction of Golgi-resident protein types by using feature selection technique, " Chemometrics and Intelligent Laboratory Systems, vol. 124, pp. 9-13, 2013.
-
(2013)
Chemometrics and Intelligent Laboratory Systems
, vol.124
, pp. 9-13
-
-
Ding, H.1
Guo, S.2
Deng, E.3
-
38
-
-
77958151520
-
Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information
-
W. Chen and H. Lin, "Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information, " Biochemical and Biophysical Research Communications, vol. 401, no. 3, pp. 382-384, 2010.
-
(2010)
Biochemical and Biophysical Research Communications
, vol.401
, Issue.3
, pp. 382-384
-
-
Chen, W.1
Lin, H.2
-
39
-
-
78650178724
-
Prediction of subcellular location of mycobacterial protein using feature selection techniques
-
H. Lin, H. Ding, F. Guo, and J. Huang, "Prediction of subcellular location of mycobacterial protein using feature selection techniques, " Molecular Diversity, vol. 14, no. 4, pp. 667-671, 2010.
-
(2010)
Molecular Diversity
, vol.14
, Issue.4
, pp. 667-671
-
-
Lin, H.1
Ding, H.2
Guo, F.3
Huang, J.4
-
40
-
-
78650209947
-
Prediction of thermophilic proteins using feature selection technique
-
H. Lin and W. Chen, "Prediction of thermophilic proteins using feature selection technique, " Journal ofMicrobiologicalMethods, vol. 84, no. 1, pp. 67-70, 2011.
-
(2011)
Journal OfMicrobiologicalMethods
, vol.84
, Issue.1
, pp. 67-70
-
-
Lin, H.1
Chen, W.2
-
41
-
-
84900463301
-
PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition
-
W. Chen, T. Y. Lei, D. C. Jin, H. Lin, and K. C. Chou, "PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition, " Analytical Biochemistry, vol. 456, pp. 53-60, 2014.
-
(2014)
Analytical Biochemistry
, vol.456
, pp. 53-60
-
-
Chen, W.1
Lei, T.Y.2
Jin, D.C.3
Lin, H.4
Chou, K.C.5
-
42
-
-
84878789801
-
Using overrepresented tetrapeptides to predict protein submitochondria locations
-
H. Lin, W. Chen, L. Yuan, Z. Li, and H. Ding, "Using overrepresented tetrapeptides to predict protein submitochondria locations, " Acta Biotheoretica, vol. 61, no. 2, pp. 259-268, 2013.
-
(2013)
Acta Biotheoretica
, vol.61
, Issue.2
, pp. 259-268
-
-
Lin, H.1
Chen, W.2
Yuan, L.3
Li, Z.4
Ding, H.5
-
43
-
-
84874229261
-
Identifying multi-functional enzyme by hierarchical multi-label classifier
-
Q. Zou, W. Chen, Y. Huang, X. Liu, and Y. Jiang, "Identifying multi-functional enzyme by hierarchical multi-label classifier, " Journal of Computational and Theoretical Nanoscience, vol. 10, no. 4, pp. 1038-1043, 2013.
-
(2013)
Journal of Computational and Theoretical Nanoscience
, vol.10
, Issue.4
, pp. 1038-1043
-
-
Zou, Q.1
Chen, W.2
Huang, Y.3
Liu, X.4
Jiang, Y.5
-
44
-
-
84881519843
-
Binmempredict: A web server and software for predicting membrane protein types
-
Q. Zou, X. Li, Y. Jiang, Y. Zhao, and G. Wang, "Binmempredict: a web server and software for predicting membrane protein types, " Current Proteomics, vol. 10, no. 1, pp. 2-9, 2013.
-
(2013)
Current Proteomics
, vol.10
, Issue.1
, pp. 2-9
-
-
Zou, Q.1
Li, X.2
Jiang, Y.3
Zhao, Y.4
Wang, G.5
-
45
-
-
84874240374
-
Hierarchical classification of protein folds using a novel ensemble classifier
-
Article ID e56499
-
C. Lin, Y. Zou, J. Qin et al., "Hierarchical classification of protein folds using a novel ensemble classifier, " PLoS ONE, vol. 8, no. 2, Article ID e56499, 2013.
-
(2013)
PLoS ONE
, vol.8
, Issue.2
-
-
Lin, C.1
Zou, Y.2
Qin, J.3
|