-
1
-
-
0345062357
-
Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function
-
Mirny L, Shakhnovich E, (1999) Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol 291: 177-196.
-
(1999)
J Mol Biol
, vol.291
, pp. 177-196
-
-
Mirny, L.1
Shakhnovich, E.2
-
2
-
-
0036681416
-
Scoring residue conservation
-
Valdar W, (2002) Scoring residue conservation. Proteins 48: 227-241.
-
(2002)
Proteins
, vol.48
, pp. 227-241
-
-
Valdar, W.1
-
3
-
-
0034843597
-
AL2CO: calculation of positional conservation in a protein sequence alignment
-
Pei J, Grishin N, (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 17: 700-712.
-
(2001)
Bioinformatics
, vol.17
, pp. 700-712
-
-
Pei, J.1
Grishin, N.2
-
4
-
-
33748505263
-
Incorporating background frequency improves entropy-based residue conservation measures
-
Wang K, Samudrala R, (2006) Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics 7: 385.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 385
-
-
Wang, K.1
Samudrala, R.2
-
5
-
-
34548133728
-
Predicting functionally important residues from sequence conservation
-
Capra J, Singh S, (2007) Predicting functionally important residues from sequence conservation. Bioinformatics 23: 1875-1882.
-
(2007)
Bioinformatics
, vol.23
, pp. 1875-1882
-
-
Capra, J.1
Singh, S.2
-
6
-
-
0346733329
-
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
-
Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES, (2004) Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 13: 190-202.
-
(2004)
Protein Sci
, vol.13
, pp. 190-202
-
-
Caffrey, D.R.1
Somaroo, S.2
Hughes, J.D.3
Mintseris, J.4
Huang, E.S.5
-
7
-
-
3042681902
-
Conseq: the identification of functionally and structurally important residues in protein sequences
-
Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, et al. (2004) Conseq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 20 (8): 1322-1324.
-
(2004)
Bioinformatics
, vol.20
, Issue.8
, pp. 1322-1324
-
-
Berezin, C.1
Glaser, F.2
Rosenberg, J.3
Paz, I.4
Pupko, T.5
-
8
-
-
70450260600
-
Several appropriate background distributions for entropy-based protein sequence conservation measures
-
Dou YC, Zheng XQ, Wang J, (2009) Several appropriate background distributions for entropy-based protein sequence conservation measures. J Theor Biol 262 (2): 317-322.
-
(2009)
J Theor Biol
, vol.262
, Issue.2
, pp. 317-322
-
-
Dou, Y.C.1
Zheng, X.Q.2
Wang, J.3
-
9
-
-
4143051195
-
Comparison of sitespecific rate-inference methods for protein sequences: Empirical bayesian methods are superior
-
Mayrose I, Graur D, Ben-Tal N, Pupko T, (2004) Comparison of sitespecific rate-inference methods for protein sequences: Empirical bayesian methods are superior. Mol Biol and Evol 21: 1781-1791.
-
(2004)
Mol Biol and Evol
, vol.21
, pp. 1781-1791
-
-
Mayrose, I.1
Graur, D.2
Ben-Tal, N.3
Pupko, T.4
-
10
-
-
35948961101
-
Predicting and annotating catalytic residues: an information theoretic approach
-
Sterner B, Singh R, Berger B, (2007) Predicting and annotating catalytic residues: an information theoretic approach. J Comput Biol 14: 1058-1073.
-
(2007)
J Comput Biol
, vol.14
, pp. 1058-1073
-
-
Sterner, B.1
Singh, R.2
Berger, B.3
-
11
-
-
49749105937
-
Estimating residue evolutionary conservation by introducing von neumann entropy and a novel gap-treating approach
-
Zhang SW, Zhang YL, Pan Q, Cheng YM, Chou KC, (2008) Estimating residue evolutionary conservation by introducing von neumann entropy and a novel gap-treating approach. Amino Acids 35: 495-501.
-
(2008)
Amino Acids
, vol.35
, pp. 495-501
-
-
Zhang, S.W.1
Zhang, Y.L.2
Pan, Q.3
Cheng, Y.M.4
Chou, K.C.5
-
12
-
-
54949145058
-
Intrepidinformation-theoretic tree traversal for protein functional site identification
-
Sankararaman S, Sjölander K, (2008) Intrepidinformation-theoretic tree traversal for protein functional site identification. Bioinformatics 24: 2445C2452.
-
(2008)
Bioinformatics
, vol.24
-
-
Sankararaman, S.1
Sjölander, K.2
-
13
-
-
11344278220
-
Predicting protein functional sites with phylogenetic motifs
-
La D, Sutch B, Livesay DR, (2005) Predicting protein functional sites with phylogenetic motifs. Proteins 58: 309-320.
-
(2005)
Proteins
, vol.58
, pp. 309-320
-
-
La, D.1
Sutch, B.2
Livesay, D.R.3
-
14
-
-
53749096681
-
Improving position-specific predictions of protein functional sites using phylogenetic motifs
-
Bahadur Dukka KC, Livesay DR, (2008) Improving position-specific predictions of protein functional sites using phylogenetic motifs. Bioinformatics 24: 2308-2316.
-
(2008)
Bioinformatics
, vol.24
, pp. 2308-2316
-
-
Bahadur Dukka, K.C.1
Livesay, D.R.2
-
16
-
-
1242339659
-
A family of evolution-entropy hybrid methods for ranking residues by importance
-
Mihalek I, Reš I, Lichtarge O, (2004) A family of evolution-entropy hybrid methods for ranking residues by importance. J Mol Biol 336: 1265-1282.
-
(2004)
J Mol Biol
, vol.336
, pp. 1265-1282
-
-
Mihalek, I.1
Reš, I.2
Lichtarge, O.3
-
17
-
-
40049091146
-
Prediction of protein functional residues from sequence by probability density estimation
-
Fischer JD, Mayer CE, Söding J, (2008) Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics 24: 613-620.
-
(2008)
Bioinformatics
, vol.24
, pp. 613-620
-
-
Fischer, J.D.1
Mayer, C.E.2
Söding, J.3
-
18
-
-
59449097392
-
Prediction of catalytic residues using the variation of stereochemical properties
-
Dou YC, Zheng XQ, Wang J, (2009) Prediction of catalytic residues using the variation of stereochemical properties. Protein J 28: 29-33.
-
(2009)
Protein J
, vol.28
, pp. 29-33
-
-
Dou, Y.C.1
Zheng, X.Q.2
Wang, J.3
-
19
-
-
78449287914
-
Prediction of catalytic residues based on an overlapping amino acid classification
-
Dou YC, Zheng XQ, Yang JL, Wang J, (2010) Prediction of catalytic residues based on an overlapping amino acid classification. Amino Acids 39: 1353-1361.
-
(2010)
Amino Acids
, vol.39
, pp. 1353-1361
-
-
Dou, Y.C.1
Zheng, X.Q.2
Yang, J.L.3
Wang, J.4
-
20
-
-
43149110628
-
Robustness of the residue conservation score reecting both frequencies and physicochemistries
-
Liu XS, Guo WL, (2008) Robustness of the residue conservation score reecting both frequencies and physicochemistries. Amino Acids 34: 643-652.
-
(2008)
Amino Acids
, vol.34
, pp. 643-652
-
-
Liu, X.S.1
Guo, W.L.2
-
21
-
-
79958069735
-
Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters
-
Williamson RM, (1995) Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters. J Theor Biol 24: 908-915.
-
(1995)
J Theor Biol
, vol.24
, pp. 908-915
-
-
Williamson, R.M.1
-
22
-
-
0037470597
-
Automatic methods for predicting functionally important residues
-
del Sol Mesa A, Pazos F, Valencia A, (2003) Automatic methods for predicting functionally important residues. J Mol Biol 326: 1289-1302.
-
(2003)
J Mol Biol
, vol.326
, pp. 1289-1302
-
-
del Sol Mesa, A.1
Pazos, F.2
Valencia, A.3
-
23
-
-
1642325994
-
Prediction of functional sites in proteins using conserved functional group analysis
-
Innis CA, Anand AP, Sowdhamini R, (2003) Prediction of functional sites in proteins using conserved functional group analysis. J Mol Biol 337: 053-1068.
-
(2003)
J Mol Biol
, vol.337
, pp. 053-1068
-
-
Innis, C.A.1
Anand, A.P.2
Sowdhamini, R.3
-
24
-
-
1842454912
-
Prediction of functional sites by analysis of sequence and structure conservation
-
Panchenko AR, Kondrashov F, Bryant S, (2003) Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci 13: 884-892.
-
(2003)
Protein Sci
, vol.13
, pp. 884-892
-
-
Panchenko, A.R.1
Kondrashov, F.2
Bryant, S.3
-
25
-
-
48849085285
-
An improved prediction of catalytic residues in enzyme structures
-
Tang YR, Sheng ZY, Chen YZ, Zhang ZD, (2008) An improved prediction of catalytic residues in enzyme structures. Protein Eng Des Sel 21: 295-302.
-
(2008)
Protein Eng Des Sel
, vol.21
, pp. 295-302
-
-
Tang, Y.R.1
Sheng, Z.Y.2
Chen, Y.Z.3
Zhang, Z.D.4
-
26
-
-
67651205773
-
Resboost: characterizing and predicting catalytic residues in enzymes
-
Alterovitz R, Arvey A, Sankararaman S, Dallett C, Freund Y, et al. (2009) Resboost: characterizing and predicting catalytic residues in enzymes. BMC Bioinformatics 10: 197.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 197
-
-
Alterovitz, R.1
Arvey, A.2
Sankararaman, S.3
Dallett, C.4
Freund, Y.5
-
27
-
-
34249308113
-
How accurate and statistically robust are catalytic site predictions based on closeness centrality?
-
Chea E, Livesay DR, (2007) How accurate and statistically robust are catalytic site predictions based on closeness centrality? BMC Bioinformatics 8: 153.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 153
-
-
Chea, E.1
Livesay, D.R.2
-
28
-
-
59149090849
-
Partial order optimum likelihood (pool): Maximum likelihood prediction of protein active site residues using 3d structure and sequence properties
-
Tong W, Wei Y, Murga LF, Ondrechen MJ, Williams RJ, (2009) Partial order optimum likelihood (pool): Maximum likelihood prediction of protein active site residues using 3d structure and sequence properties. PLoS Comput Biol 5 (1): e1000266.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.1
-
-
Tong, W.1
Wei, Y.2
Murga, L.F.3
Ondrechen, M.J.4
Williams, R.J.5
-
29
-
-
55449117336
-
Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures
-
Gong S, Blundell TL, (2008) Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures. PLoS Comput Biol 4 (10): e1000179.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.10
-
-
Gong, S.1
Blundell, T.L.2
-
30
-
-
78649655423
-
Networks of high mutual information define the structural proximity of catalytic sites: Implications for catalytic residue identification
-
Marino Buslje C, Teppa E, Di Domenico T, Delfino JM, Nielsen M, (2010) Networks of high mutual information define the structural proximity of catalytic sites: Implications for catalytic residue identification. PLoS Comput Biol 6 (11): e1000978.
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.11
-
-
Marino Buslje, C.1
Teppa, E.2
Di Domenico, T.3
Delfino, J.M.4
Nielsen, M.5
-
31
-
-
34547575992
-
firestarprediction of functionally important residues using structural templates and alignment reliability
-
Lopez G, A V, Tress M, (2007) firestarprediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res 35: W573-W577.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Lopez, G.1
Tress, M.2
-
32
-
-
34249676832
-
Prediction of functional sites based on the fuzzy oil drop model
-
Brylinski M, Prymula K, Jurkowski W, Kochanczyk M, Stawowczyk E, et al. (2007) Prediction of functional sites based on the fuzzy oil drop model. PLoS Comput Biol 3 (5): e94.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.5
-
-
Brylinski, M.1
Prymula, K.2
Jurkowski, W.3
Kochanczyk, M.4
Stawowczyk, E.5
-
33
-
-
0042674397
-
Using a neural network and spatial clustering to predict the location of active sites in enzymes
-
Gutteridge A, Bartlett GJ, Thornton JM, (2003) Using a neural network and spatial clustering to predict the location of active sites in enzymes. J Mol Biol 303: 719-734.
-
(2003)
J Mol Biol
, vol.303
, pp. 719-734
-
-
Gutteridge, A.1
Bartlett, G.J.2
Thornton, J.M.3
-
34
-
-
84868117026
-
Prediction of enzyme catalytic sites from sequence using neural networks
-
Pande S, Raheja A, Livesay DR, (2007) Prediction of enzyme catalytic sites from sequence using neural networks. IEEE symposium on CIBCB 07: 247-253.
-
(2007)
IEEE Symposium on CIBCB
, vol.7
, pp. 247-253
-
-
Pande, S.1
Raheja, A.2
Livesay, D.R.3
-
35
-
-
33746950964
-
Prediction of catalytic residues using support vector machines with selected protein sequence and structural properties
-
Petrova N, Wu C, (2006) Prediction of catalytic residues using support vector machines with selected protein sequence and structural properties. BMC Bioinformatics 7: 312.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 312
-
-
Petrova, N.1
Wu, C.2
-
36
-
-
33846554792
-
Evaluation of features for catalytic residue prediction in novel folds
-
Youn E, (2007) Evaluation of features for catalytic residue prediction in novel folds. Protein Sci 16: 216-226.
-
(2007)
Protein Sci
, vol.16
, pp. 216-226
-
-
Youn, E.1
-
37
-
-
53749083563
-
Accutate sequence-based prediction of catalytic residues
-
Zhang T, Zhang H, Chen K, Shen SY, Ruan JS, et al. (2008) Accutate sequence-based prediction of catalytic residues. Bioinformatics 24: 2329-2338.
-
(2008)
Bioinformatics
, vol.24
, pp. 2329-2338
-
-
Zhang, T.1
Zhang, H.2
Chen, K.3
Shen, S.Y.4
Ruan, J.S.5
-
38
-
-
77949602893
-
Active site prediction using evolutionary and structural information
-
Sankararaman S, Sha F, Kirsch JF, Jordan MI, Sjölander K, (2010) Active site prediction using evolutionary and structural information. Bioinformatics 5: 617-624.
-
(2010)
Bioinformatics
, vol.5
, pp. 617-624
-
-
Sankararaman, S.1
Sha, F.2
Kirsch, J.F.3
Jordan, M.I.4
Sjölander, K.5
-
39
-
-
77951192988
-
Automatic prediction of catalytic residues by modeling residue structural neighborhood
-
Cilia E, Passerini A, (2010) Automatic prediction of catalytic residues by modeling residue structural neighborhood. BMC Bioinformatics 11: 115.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 115
-
-
Cilia, E.1
Passerini, A.2
-
40
-
-
77958500041
-
Metric learning for enzyme active-site search
-
Kato T, Nagano N, (2010) Metric learning for enzyme active-site search. Bioinformatics 26: 2698-2704.
-
(2010)
Bioinformatics
, vol.26
, pp. 2698-2704
-
-
Kato, T.1
Nagano, N.2
-
41
-
-
34547688865
-
An interior-point method for large-scale l1-regularized logistic regression
-
Koh K, Kim SJ, Boyd S, (2007) An interior-point method for large-scale l1-regularized logistic regression. J Mach Learn Res 8: 1519-1555.
-
(2007)
J Mach Learn Res
, vol.8
, pp. 1519-1555
-
-
Koh, K.1
Kim, S.J.2
Boyd, S.3
-
42
-
-
0035896024
-
Consurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
-
Armon A, Graur D, Ben-Tal N, (2001) Consurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 307: 447-463.
-
(2001)
J Mol Biol
, vol.307
, pp. 447-463
-
-
Armon, A.1
Graur, D.2
Ben-Tal, N.3
-
43
-
-
0036435882
-
Analysis of catalytic residues in enzyme active sites
-
Bartlett GJ, Porter CT, Borkakoti N, Thornton JM, (2002) Analysis of catalytic residues in enzyme active sites. J Mol Biol 324: 105-121.
-
(2002)
J Mol Biol
, vol.324
, pp. 105-121
-
-
Bartlett, G.J.1
Porter, C.T.2
Borkakoti, N.3
Thornton, J.M.4
-
44
-
-
0345864027
-
The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data
-
Porter C, Bartlett G, Thornton J, (2003) The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32: D129-D133.
-
(2003)
Nucleic Acids Res
, vol.32
-
-
Porter, C.1
Bartlett, G.2
Thornton, J.3
-
45
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The protein data bank. Nucleic Acids Res 28: 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
46
-
-
0030801002
-
Gapped blast and psi-blast: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped blast and psi-blast: a new generation of protein database search programs. 17 Nucleic Acids Res 25 pp. 3398-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3398-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
47
-
-
0022591495
-
The classification of amino acid conservation
-
Taylor W, (1986) The classification of amino acid conservation. J Theor Biol 119: 205-218.
-
(1986)
J Theor Biol
, vol.119
, pp. 205-218
-
-
Taylor, W.1
-
48
-
-
0021112868
-
Correlation of sequence hydrophobicities measures similarity in three dimensional protein structure
-
Sweet RM, Eisenberg D, (1983) Correlation of sequence hydrophobicities measures similarity in three dimensional protein structure. J Mol Biol 171: 479-488.
-
(1983)
J Mol Biol
, vol.171
, pp. 479-488
-
-
Sweet, R.M.1
Eisenberg, D.2
-
49
-
-
0034044314
-
The psipred protein structure prediction server
-
McGuffin LJ, Bryson K, Jones DT, (2000) The psipred protein structure prediction server. Bioinformatics 16: 404-405.
-
(2000)
Bioinformatics
, vol.16
, pp. 404-405
-
-
McGuffin, L.J.1
Bryson, K.2
Jones, D.T.3
-
50
-
-
0141506111
-
RVP-net: online prediction of real valued accessible surface area of proteins from single sequences
-
Ahmad S, Gromiha MM, Sarai A, (2003) RVP-net: online prediction of real valued accessible surface area of proteins from single sequences. Bioinformatics 19 (14): 1849-1851.
-
(2003)
Bioinformatics
, vol.19
, Issue.14
, pp. 1849-1851
-
-
Ahmad, S.1
Gromiha, M.M.2
Sarai, A.3
-
51
-
-
2542445427
-
Consurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
-
Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, et al. (2008) Consurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164.
-
(2008)
Bioinformatics
, vol.19
, pp. 163-164
-
-
Glaser, F.1
Pupko, T.2
Paz, I.3
Bell, R.E.4
Bechor-Shental, D.5
-
52
-
-
23144448512
-
Consurf 2005: the projection of evolutionary conservation scores of residues on protein structures
-
Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, et al. (2005) Consurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33: W299-W302.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Landau, M.1
Mayrose, I.2
Rosenberg, Y.3
Glaser, F.4
Martz, E.5
-
53
-
-
31344454903
-
Persistence in high-dimensional predictor selection and the virtue of overparametrization
-
Greenshtein E, Ritov Y, (2004) Persistence in high-dimensional predictor selection and the virtue of overparametrization. Bernoulli 10: 971-988.
-
(2004)
Bernoulli
, vol.10
, pp. 971-988
-
-
Greenshtein, E.1
Ritov, Y.2
-
54
-
-
33845263263
-
On model selection consistency of lasso
-
Zhao P, Yu B, (2006) On model selection consistency of lasso. J Mach Learn Res 7: 2541-2563.
-
(2006)
J Mach Learn Res
, vol.7
, pp. 2541-2563
-
-
Zhao, P.1
Yu, B.2
-
55
-
-
51049121146
-
High-dimensional generalized linear models and the lasso
-
van de Geer SA, (2008) High-dimensional generalized linear models and the lasso. Ann Stat 36: 614-645.
-
(2008)
Ann Stat
, vol.36
, pp. 614-645
-
-
van de Geer, S.A.1
-
56
-
-
77954185426
-
Prediction of protein-rna binding sites by a random forest method with combined features
-
Liu ZP, Wu LY, Wang Y, Zhang XS, Chen LN, (2010) Prediction of protein-rna binding sites by a random forest method with combined features. Bioinformatics 26: 1616-1622.
-
(2010)
Bioinformatics
, vol.26
, pp. 1616-1622
-
-
Liu, Z.P.1
Wu, L.Y.2
Wang, Y.3
Zhang, X.S.4
Chen, L.N.5
-
57
-
-
46049119818
-
StAR: a simple tool for the statistical comparison of roc curves
-
Vergara IA, Norambuena T, Ferrada E, Slater AW, Melo F, (2008) StAR: a simple tool for the statistical comparison of roc curves. BMC Bioinformatics 9: 265.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 265
-
-
Vergara, I.A.1
Norambuena, T.2
Ferrada, E.3
Slater, A.W.4
Melo, F.5
|