-
1
-
-
33846036096
-
The worldwide protein data bank (wwPDB): Ensuring a single. uniform archive of PDB data
-
Database issue
-
Berman, H., Henrick, K., Nakamura, H., Markley, J. L.: The Worldwide Protein Data Bank (wwPDB): Ensuring a Single. Uniform Archive of PDB Data. Nucleic Acids Res. 35 (Database issue), D301-303 (2007)
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
Markley, J.L.4
-
2
-
-
0034823943
-
Statistical analysis of atomic contacts at RNA-protein interfaces
-
Treger, M., Westhof, E.: Statistical Analysis of Atomic Contacts at RNA-protein Interfaces. J Mol. Recognit. 14, 199-214 (2001)
-
(2001)
J. Mol. Recognit
, vol.14
, pp. 199-214
-
-
Treger, M.1
Westhof, E.2
-
3
-
-
0035865891
-
Protein-RNA interactions: A structural analysis
-
Jones, S., Daley, D. T., Luscombe, N. M., Berman, H. M., Thornton, J. M.: Protein-RNA Interactions: a Structural Analysis. Nucleic Acids Res. 29, 943-954 (2001)
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 943-954
-
-
Jones, S.1
Daley, D.T.2
Luscombe, N.M.3
Berman, H.M.4
Thornton, J.M.5
-
4
-
-
27344440132
-
Chakrabarti conservation and relative importance of residues across protein-protein interfaces
-
Guharoy, M.: Chakrabarti Conservation and Relative Importance of Residues Across Protein-protein Interfaces. Proc. Natl. Acad. Sci. U. S. A. 102, 15447-15452 (2005)
-
(2005)
Proc. Natl. Acad. Sci. U. S. A
, vol.102
, pp. 15447-15452
-
-
Guharoy, M.1
-
5
-
-
1442323773
-
Intermolecular and intramolecular readout mechanisms in protein-DNA recognition
-
Gromiha, M. M., Siebers, J. G., Selvaraj, S., Kono, H., Sarai, A.: Intermolecular and Intramolecular Readout Mechanisms in Protein-DNA Recognition. J. Mol. Biol. 337, 285-294 (2004)
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 285-294
-
-
Gromiha, M.M.1
Siebers, J.G.2
Selvaraj, S.3
Kono, H.4
Sarai, A.5
-
6
-
-
33750997616
-
Protein-RNA interactions: Exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
-
Morozova, N., Allers, J., Myers, J., Shamoo, Y.: Protein-RNA Interactions: Exploring Binding Patterns with a Three-dimensional Superposition Analysis of High Resolution Structures. Bioinformatics 22, 2746-2752 (2006)
-
(2006)
Bioinformatics
, vol.22
, pp. 2746-2752
-
-
Morozova, N.1
Allers, J.2
Myers, J.3
Shamoo, Y.4
-
7
-
-
34247586171
-
Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
-
Shoemaker, B. A., Panchenko, A. R.: Deciphering Protein-protein Interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput. Biol. 3, 43 (2006)
-
(2006)
PLoS Comput. Biol.
, vol.3
, pp. 43
-
-
Shoemaker, B.A.1
Panchenko, A.R.2
-
8
-
-
33847042739
-
Protein-RNA interactions: Structural analysis and functional classes
-
Ellis, J. J., Broom, M., Jones, S.: Protein-RNA Interactions: Structural Analysis and Functional Classes. Proteins 66, 903-911 (2007)
-
(2007)
Proteins
, vol.66
, pp. 903-911
-
-
Ellis, J.J.1
Broom, M.2
Jones, S.3
-
9
-
-
70350782360
-
How do transcription factors select specific binding sites in the genome?
-
Pan, Y., Tsai, C. J., Ma, B., Nussinov, R.: How Do Transcription Factors Select Specific Binding Sites in the Genome? Nat. Struct. Mol. Biol. 16, 1118-1120 (2009)
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 1118-1120
-
-
Pan, Y.1
Tsai, C.J.2
Ma, B.3
Nussinov, R.4
-
10
-
-
72949113228
-
Energy based approach for understanding the recognition mechanism in protein-protein complexes
-
Gromiha, M. M., Yokota, K., Fukui, K.: Energy Based Approach for Understanding the Recognition Mechanism in Protein-protein Complexes. Mol. Biosyst. 5, 1779-1786 (2009)
-
(2009)
Mol. Biosyst
, vol.5
, pp. 1779-1786
-
-
Gromiha, M.M.1
Yokota, K.2
Fukui, K.3
-
11
-
-
59149087824
-
Prediction of protein-protein interaction sites in sequences and 3D structures by random forests
-
Sikić, M., Tomić, S., Vlahovicek, K.: Prediction of Protein-protein Interaction Sites in Sequences and 3D Structures by Random Forests. PLoS Comput. Biol. 5, e1000278 (2009)
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Sikić, M.1
Tomić, S.2
Vlahovicek, K.3
-
12
-
-
1842765629
-
Prediction of protein-protein interaction sites using support vector machines
-
Koike, A., Takagi, T.: Prediction of Protein-protein Interaction Sites Using Support Vector Machines. Protein. Eng. Des. Sel. 17, 165-173 (2004)
-
(2004)
Protein. Eng. Des. Sel.
, vol.17
, pp. 165-173
-
-
Koike, A.1
Takagi, T.2
-
13
-
-
33846662784
-
ISIS: Interaction sites identified from sequence
-
Ofran, Y., Rost, B.: ISIS: Interaction Sites Identified From Sequence. Bioinformatics 23(2), e13-6 (2007)
-
(2007)
Bioinformatics
, vol.23
, Issue.2
-
-
Ofran, Y.1
Rost, B.2
-
14
-
-
34547560560
-
RNABindR: A server for analyzing and predicting RNA-binding sites in proteins
-
Web Server issue
-
Terribilini, M., Sander, J. D., Lee, J. H., Zaback, P., Jernigan, R. L., Honavar, V., Dobbs, D.: RNABindR: A Server for Analyzing and Predicting RNA-binding Sites in Proteins. Nucleic Acids Res. 35 (Web Server issue), W578-W584 (2007)
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Terribilini, M.1
Sander, J.D.2
Lee, J.H.3
Zaback, P.4
Jernigan, R.L.5
Honavar, V.6
Dobbs, D.7
-
15
-
-
33747828217
-
BindN: A web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences
-
Web Server issue
-
Wang, L., Brown, S. J.: BindN: A web-based Tool for Efficient Prediction of DNA and RNA Binding Sites in Amino Acid Sequences. Nucleic. Acids Res. 34 (Web Server issue), W243-W248 (2006)
-
(2006)
Nucleic. Acids Res.
, vol.34
-
-
Wang, L.1
Brown, S.J.2
-
16
-
-
40549105098
-
Prediction of RNA binding sites in a protein using SVM and PSSM profile
-
Kumar, M., Gromiha, M. M., Raghava, G. P.: Prediction of RNA Binding Sites in a Protein Using SVM and PSSM Profile. Proteins 71, 189-194 (2008)
-
(2008)
Proteins
, vol.71
, pp. 189-194
-
-
Kumar, M.1
Gromiha, M.M.2
Raghava, G.P.3
-
17
-
-
1542400269
-
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
-
Ahmad, S., Gromiha, M. M., Sarai, A.: Analysis and Prediction of DNA-binding Proteins and Their Binding Residues Based on Composition, Sequence and Structural Information. Bioinformatics 20, 477-486 (2004)
-
(2004)
Bioinformatics
, vol.20
, pp. 477-486
-
-
Ahmad, S.1
Gromiha, M.M.2
Sarai, A.3
-
18
-
-
34547852238
-
Prediction of DNA-binding residues from sequence
-
Ofran, Y., Mysore, V., Rost, B.: Prediction of DNA-binding Residues from Sequence. Bioinformatics 53, i347-i353 (2007)
-
(2007)
Bioinformatics
, vol.53
-
-
Ofran, Y.1
Mysore, V.2
Rost, B.3
-
19
-
-
77949330477
-
Sequence and structural analysis of binding site residues in protein-protein complexes
-
Gromiha, M. M., Yokota, K., Fukui, K.: Sequence and Structural Analysis of Binding Site Residues in Protein-protein Complexes. Int. J. Biol. Macromol. 46, 187-192 (2010)
-
(2010)
Int. J. Biol. Macromol.
, vol.46
, pp. 187-192
-
-
Gromiha, M.M.1
Yokota, K.2
Fukui, K.3
-
20
-
-
43349105225
-
Dissecting protein-RNA recognition sites
-
Bahadur, R. P., Zacharias, M., Janin, J.: Dissecting Protein-RNA Recognition Sites. Nucleic Acids Res. 36, 2705-2716 (2008)
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 2705-2716
-
-
Bahadur, R.P.1
Zacharias, M.2
Janin, J.3
-
21
-
-
68049118950
-
An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles
-
Xu, B., Yang, Y., Liang, H., Zhou, Y.: An All-atom Knowledge-based Energy Function for Protein-DNA Threading, Docking Decoy Discrimination, and Prediction of Transcription-Factor Binding Profiles. Proteins 76, 718-730 (2009)
-
(2009)
Proteins
, vol.76
, pp. 718-730
-
-
Xu, B.1
Yang, Y.2
Liang, H.3
Zhou, Y.4
-
22
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., Kollman, P. A.: A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Amer. Chem. Soc. 117, 5179-5197 (1995)
-
(1995)
J. Amer. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
23
-
-
0033532946
-
Free-energy maps of base-amino acid interactions for DNA-protein recognition
-
Pichierri, F., Aida, M., Gromiha, M. M., Sarai, A.: Free-Energy Maps of Base-Amino Acid Interactions for DNA-Protein Recognition. J. Amer. Chem. Soc. 121, 6152-6157 (1999)
-
(1999)
J. Amer. Chem. Soc.
, vol.121
, pp. 6152-6157
-
-
Pichierri, F.1
Aida, M.2
Gromiha, M.M.3
Sarai, A.4
-
24
-
-
77958513784
-
Understanding the recognition mechanism in protein-RNA complexes using energy based approach
-
in press
-
Gromiha, M. M., Yokota, K., Fukui, K.: Understanding the Recognition Mechanism in Protein-RNA Complexes Using Energy Based Approach. Curr. Protein Pept. Sci., (in press, 2010)
-
(2010)
Curr. Protein Pept. Sci.
-
-
Gromiha, M.M.1
Yokota, K.2
Fukui, K.3
-
25
-
-
33644878621
-
PINT: Protein-protein interactions thermodynamic database
-
Kumar, M. D., Gromiha, M. M.: PINT: Protein-protein Interactions Thermodynamic Database. Nucleic Acids Res. 34, D195-D198 (2006)
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Kumar, M.D.1
Gromiha, M.M.2
-
26
-
-
0035176895
-
Thermodynamic database for protein-nucleic acid interactions(ProNIT)
-
Prabakaran, P., An, J., Gromiha, M. M., Selvaraj, S., Uedaira, H., Kono, H., Sarai, A.: Thermodynamic Database for Protein-nucleic Acid Interactions (ProNIT). Bioinformatics 17, 1027-1034 (2001) (Pubitemid 33085609)
-
(2001)
Bioinformatics
, vol.17
, Issue.11
, pp. 1027-1034
-
-
Prabakaran, P.1
An, J.2
Gromiha, M.M.3
Selvaraj, S.4
Uedaira, H.5
Kono, H.6
Sarai, A.7
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