-
1
-
-
11844249426
-
Hot regions in protein-protein interactions: The organization and contribution of structurally conserved hot spot residues
-
Keskin,O., Ma,B. and Nussinov,R. (2005) Hot regions in protein-protein interactions: The organization and contribution of structurally conserved hot spot residues. J. Mol. Biol., 345, 1281-1294.
-
(2005)
J. Mol. Biol
, vol.345
, pp. 1281-1294
-
-
Keskin, O.1
Ma, B.2
Nussinov, R.3
-
2
-
-
27344440132
-
Conservation and relative importance of residues across protein-protein interfaces
-
Guharoy,M. and Chakrabarti,P. (2005) Conservation and relative importance of residues across protein-protein interfaces. Proc. Natl Acad. Sci. USA, 102, 15447-15452.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15447-15452
-
-
Guharoy, M.1
Chakrabarti, P.2
-
3
-
-
33745597909
-
Predicting protein interaction sites: Binding hot-spots in protein-protein and protein-ligand interfaces
-
Burgoyne,N.J. and Jackson,R.M. (2006) Predicting protein interaction sites: Binding hot-spots in protein-protein and protein-ligand interfaces. Bioinformatics, 22, 1335-1342.
-
(2006)
Bioinformatics
, vol.22
, pp. 1335-1342
-
-
Burgoyne, N.J.1
Jackson, R.M.2
-
4
-
-
0037195144
-
Simple physical model for binding energy hot spots in protein-protein complexes
-
Kortemme,T. and Baker,D.A. (2002) Simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl Acad. Sci. USA, 99, 14116-14121.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 14116-14121
-
-
Kortemme, T.1
Baker, D.A.2
-
5
-
-
0037609791
-
Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
-
Ma,B., Elkayam,T., Wolfson,H. and Nussinov,R. (2003) Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl Acad. Sci. USA 100, 5772-5777.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 5772-5777
-
-
Ma, B.1
Elkayam, T.2
Wolfson, H.3
Nussinov, R.4
-
6
-
-
0028916599
-
A hot spot of binding energy in a hormone-receptor interface
-
Clackson,T. and Wells,J.A. (1995) A hot spot of binding energy in a hormone-receptor interface. Science, 267, 383-386.
-
(1995)
Science
, vol.267
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
7
-
-
7944225979
-
Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking
-
Li,X., Keskin,O., Ma,B., Nussinov,R. and Liang,J. (2004) Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J. Mol. Biol., 344, 781-795.
-
(2004)
J. Mol. Biol
, vol.344
, pp. 781-795
-
-
Li, X.1
Keskin, O.2
Ma, B.3
Nussinov, R.4
Liang, J.5
-
8
-
-
24644517567
-
Effective function annotation through catalytic residue conservation
-
George,R.A., Spriggs,R.V., Bartlett,G.J., Gutteridge,A., Macartur,M.W., Porter,C.T., Al-Lazikani,B., Thornton,J.M. and Swindelss,M.B. (2005) Effective function annotation through catalytic residue conservation. Proc. Natl Acad. Sci. USA, 102, 12299-12304.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 12299-12304
-
-
George, R.A.1
Spriggs, R.V.2
Bartlett, G.J.3
Gutteridge, A.4
Macartur, M.W.5
Porter, C.T.6
Al-Lazikani, B.7
Thornton, J.M.8
Swindelss, M.B.9
-
9
-
-
33745889333
-
Folding of Cu/Zn superoxide dismutase suggests structural hotspots for gain of neurotoxic function in ALS: Parallels to precursors in amyloid disease
-
Nordlund,A. and Oliveberg,M. (2006) Folding of Cu/Zn superoxide dismutase suggests structural hotspots for gain of neurotoxic function in ALS: Parallels to precursors in amyloid disease. Proc. Natl Acad. Sci. USA, 103, 10218-10223.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 10218-10223
-
-
Nordlund, A.1
Oliveberg, M.2
-
10
-
-
33846351302
-
Precise physical models of protein-DNA interaction from high-throughput data
-
Kinney,J.B., Tkacik,G. and Callan,C.G. Jr. (2007) Precise physical models of protein-DNA interaction from high-throughput data. Proc. Natl Acad. Sci. USA, 104, 501-506.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 501-506
-
-
Kinney, J.B.1
Tkacik, G.2
Callan Jr., C.G.3
-
11
-
-
41149090794
-
Algorithm for prediction of tumour suppressor p53 affmity for binding sites in DNA
-
Veprintsev,D.B. and Fersht,A.R. (2008) Algorithm for prediction of tumour suppressor p53 affmity for binding sites in DNA. Nucleic Acids Res., 36, 1589-1598.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 1589-1598
-
-
Veprintsev, D.B.1
Fersht, A.R.2
-
12
-
-
34547830863
-
Inferring protein-DNA dependencies using motif alignments and mutual information
-
Mahony,S., Auron,P.E. and Benos,P.V. (2007) Inferring protein-DNA dependencies using motif alignments and mutual information. Bioinformatics, 23, 297-304.
-
(2007)
Bioinformatics
, vol.23
, pp. 297-304
-
-
Mahony, S.1
Auron, P.E.2
Benos, P.V.3
-
13
-
-
1542400269
-
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
-
Ahmad,S., Gromiha,M.M. and Sarai,A. (2004) Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics, 20, 477-486.
-
(2004)
Bioinformatics
, vol.20
, pp. 477-486
-
-
Ahmad, S.1
Gromiha, M.M.2
Sarai, A.3
-
14
-
-
25444524842
-
PSSM-based prediction of DNA binding sites in proteins
-
Ahmad,S. and Sarai,A. (2005) PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics, 6, 33.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 33
-
-
Ahmad, S.1
Sarai, A.2
-
15
-
-
33747827908
-
ReadOut: Structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition
-
Ahmad,S., Kono,H., Arauzo-Bravo,M.J. and Sarai,A. (2006) ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. Nucleic Acids Res., 34, W124-W127.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Ahmad, S.1
Kono, H.2
Arauzo-Bravo, M.J.3
Sarai, A.4
-
16
-
-
4143064791
-
Moment-based prediction of DNA-binding proteins
-
Ahmad,S. and Sarai,A. (2004) Moment-based prediction of DNA-binding proteins. J. Mol. Biol., 341, 65-71.
-
(2004)
J. Mol. Biol
, vol.341
, pp. 65-71
-
-
Ahmad, S.1
Sarai, A.2
-
17
-
-
2942620218
-
Predicting indirect readout effects in protein-DNA interactions
-
Zhang,Y., Xi,Z., Hegde,R.S., Shakked,Z. and Crothers,D.M. (2004) Predicting indirect readout effects in protein-DNA interactions. Proc. Natl Acad. Sci. USA, 101, 8337-8341.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 8337-8341
-
-
Zhang, Y.1
Xi, Z.2
Hegde, R.S.3
Shakked, Z.4
Crothers, D.M.5
-
18
-
-
30344439849
-
Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity
-
Hallikas,O., Palin,K., Sinjushina,N., Rautiainen,R., Partanen,J., Ukkonen,E. and Taipale,J. (2006) Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell, 124, 47-59.
-
(2006)
Cell
, vol.124
, pp. 47-59
-
-
Hallikas, O.1
Palin, K.2
Sinjushina, N.3
Rautiainen, R.4
Partanen, J.5
Ukkonen, E.6
Taipale, J.7
-
19
-
-
34547852238
-
Prediction of DNA-binding residues from sequence
-
Ofran,Y., Mysore,V. and Rost,B. (2007) Prediction of DNA-binding residues from sequence, Bioinformatics, 23, 347-353.
-
(2007)
Bioinformatics
, vol.23
, pp. 347-353
-
-
Ofran, Y.1
Mysore, V.2
Rost, B.3
-
20
-
-
0034682882
-
Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
-
Pabo,C.O. and Nekludova,L. (2000) Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition? J. Mol. Biol., 301, 597-624.
-
(2000)
J. Mol. Biol
, vol.301
, pp. 597-624
-
-
Pabo, C.O.1
Nekludova, L.2
-
21
-
-
0037109192
-
Additivity in protein-DNA interactions: How good an approximation is it?
-
Benos,P.V., Bulyk,M.L. and Stormo,G.D. (2002) Additivity in protein-DNA interactions: How good an approximation is it? Nucleic Acids Res., 30, 4442-4451.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4442-4451
-
-
Benos, P.V.1
Bulyk, M.L.2
Stormo, G.D.3
-
22
-
-
34547842521
-
Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism
-
Faiger,H., Ivanchenko,M. and Haran,T.E. (2007) Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism. Nucleic Acids Res. 35, 4409-4419.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 4409-4419
-
-
Faiger, H.1
Ivanchenko, M.2
Haran, T.E.3
-
23
-
-
19544366293
-
Non-additivity in protein-DNA binding
-
O'Flanagan,R.A., Paillard,G., Lavery,R. and Sengupta,A.M. (2005) Non-additivity in protein-DNA binding. Bioinformatics, 21, 2254-2263.
-
(2005)
Bioinformatics
, vol.21
, pp. 2254-2263
-
-
O'Flanagan, R.A.1
Paillard, G.2
Lavery, R.3
Sengupta, A.M.4
-
24
-
-
0036529540
-
Structural analysis of conserved base-pairs in protein-DNA complexes
-
Mirny,L.A. and Gelfand,M.S. (2002) Structural analysis of conserved base-pairs in protein-DNA complexes, Nucleic Acids Res., 30, 1704-1711.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1704-1711
-
-
Mirny, L.A.1
Gelfand, M.S.2
-
25
-
-
25444480735
-
Quantitative analysis of EGR proteins binding to DNA: Assessing additivity in both the binding site and the protein
-
Liu,J. and Stormo,G.D. (2005) Quantitative analysis of EGR proteins binding to DNA: Assessing additivity in both the binding site and the protein. BMC Bioinformatics, 6, 176.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 176
-
-
Liu, J.1
Stormo, G.D.2
-
26
-
-
4043129033
-
Interaction of DNA with clusters of amino acids in proteins
-
Sathyapriya,R. and Vishveshwara,S. (2004) Interaction of DNA with clusters of amino acids in proteins. Nucleic Acids Res., 32, 4109-4118.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 4109-4118
-
-
Sathyapriya, R.1
Vishveshwara, S.2
-
27
-
-
33644874615
-
ProTherm and ProNIT: Thermodynamic databases for proteins and protein-nucleic acid interactions
-
Kumar,M.D., Bava,K.A., Gromiha,M.M., Prabakaran,P., Kitajima,K., Uedaira,H. and Sarai,A. (2006) ProTherm and ProNIT: Thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res., 34, D204-D206.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kumar, M.D.1
Bava, K.A.2
Gromiha, M.M.3
Prabakaran, P.4
Kitajima, K.5
Uedaira, H.6
Sarai, A.7
-
28
-
-
0033954256
-
The Protein Data Bank
-
Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Boume,P.E. (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
Weissig, H.6
Shindyalov, I.N.7
Boume, P.E.8
-
29
-
-
0025183708
-
Basic local alignment search tool
-
Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
30
-
-
33746748243
-
An overview of the structures of protein-DNA complexes
-
Luscombe,N.M., Austin,S.E., Berman,H.M. and Thornton,J.M. (2000) An overview of the structures of protein-DNA complexes. Genome Biol., 1, 1.
-
(2000)
Genome Biol
, vol.1
, pp. 1
-
-
Luscombe, N.M.1
Austin, S.E.2
Berman, H.M.3
Thornton, J.M.4
-
31
-
-
36448991500
-
-
Larkin,M.,A, Blackshields,G, Brown,N.P, Chenna,R, McGettigan,P.A, McWilliam,H, Valentin,F, Wallace,I.M, Wilm,A, Lopez,R. et al, 2007 ClustalW2 and ClustalX version 2. Bioinformatics, 23, 2947-2948
-
Larkin,M.,A., Blackshields,G., Brown,N.P., Chenna,R., McGettigan,P.A., McWilliam,H., Valentin,F., Wallace,I.M., Wilm,A., Lopez,R. et al. (2007) ClustalW2 and ClustalX version 2. Bioinformatics, 23, 2947-2948.
-
-
-
-
32
-
-
0026656815
-
Exhaustive matching of the entire protein sequence database
-
Gonnet,G.H., Cohen,M.A. and Benner,S.A. (1992) Exhaustive matching of the entire protein sequence database. Science, 256, 1443-1145.
-
(1992)
Science
, vol.256
, pp. 1443-1145
-
-
Gonnet, G.H.1
Cohen, M.A.2
Benner, S.A.3
-
33
-
-
0036681416
-
Scoring residue conservation
-
Valdar,W.S. (2002) Scoring residue conservation. Proteins, 48 227-241.
-
(2002)
Proteins
, vol.48
, pp. 227-241
-
-
Valdar, W.S.1
-
34
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bond and geometrical features
-
Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bond and geometrical features. Bippolymers, 22, 2577-2637.
-
(1983)
Bippolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
35
-
-
34249898391
-
SVM-Cabins: Prediction of solvent accessibility using accumulation cutoff set and support vector machine
-
Wang,J.Y., Lee,H.M. and Ahmad,S. (2007) SVM-Cabins: Prediction of solvent accessibility using accumulation cutoff set and support vector machine. Proteins, 68, 82-91.
-
(2007)
Proteins
, vol.68
, pp. 82-91
-
-
Wang, J.Y.1
Lee, H.M.2
Ahmad, S.3
-
36
-
-
1542400269
-
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
-
Ahmad,S., Gromiha,M.M. and Sarai,A. (2004) Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics, 20, 477-486.
-
(2004)
Bioinformatics
, vol.20
, pp. 477-486
-
-
Ahmad, S.1
Gromiha, M.M.2
Sarai, A.3
-
37
-
-
56349144356
-
Benchmarking and analysis of DNA-binding site prediction using machine learning
-
June 1-8, Hong Kong, IEEE. pp
-
Andrabi,M., Ahmad,S., Mizuguchi,K., and Sarai,A. (2008) Benchmarking and analysis of DNA-binding site prediction using machine learning. In Proceedings of International Joint Conference on Neural Networks (IJCNN), World Conference on Computational Intelligence (WCCI), June 1-8, Hong Kong, IEEE. pp. 1746-1750
-
(2008)
Proceedings of International Joint Conference on Neural Networks (IJCNN), World Conference on Computational Intelligence (WCCI)
, pp. 1746-1750
-
-
Andrabi, M.1
Ahmad, S.2
Mizuguchi, K.3
Sarai, A.4
|