-
1
-
-
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, 943-54 (2001). (Pubitemid 32162263)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.4
, pp. 943-954
-
-
Jones, S.1
Daley, D.T.A.2
Luscombe, N.M.3
Berman, H.M.4
Thornton, J.M.5
-
2
-
-
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, 903-11 (2007).
-
(2007)
Proteins
, vol.66
, pp. 903-911
-
-
Ellis, J.J.1
Broom, M.2
Jones, S.3
-
3
-
-
4944226552
-
A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys
-
DOI 10.1093/nar/gkh785
-
Chen, Y., Kortemme, T., Robertson, T., Baker, D. & Varani, G. A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res 32, 5147-62 (2004). (Pubitemid 39445502)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.17
, pp. 5147-5162
-
-
Chen, Y.1
Kortemme, T.2
Robertson, T.3
Baker, D.4
Varani, G.5
-
4
-
-
84868295514
-
Automated and fast building of three-dimensional RNA structures
-
Zhao, Y. et al. Automated and fast building of three-dimensional RNA structures. Sci Rep 2, 734 (2012).
-
(2012)
Sci Rep
, vol.2
, pp. 734
-
-
Zhao, Y.1
-
5
-
-
83555179181
-
A new residue-nucleotide propensity potential with structural information considered for discriminating protein-RNA docking decoys
-
Li, C. H., Cao, L. B., Su, J. G., Yang, Y. X. & Wang, C. X. A new residue-nucleotide propensity potential with structural information considered for discriminating protein-RNA docking decoys. Proteins 80, 14-24 (2012).
-
(2012)
Proteins
, vol.80
, pp. 14-24
-
-
Li, C.H.1
Cao, L.B.2
Su, J.G.3
Yang, Y.X.4
Wang, C.X.5
-
6
-
-
80051788801
-
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking
-
Tuszynska, I. & Bujnicki, J. M. DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking. BMC Bioinformatics 12, 348 (2011).
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 348
-
-
Tuszynska, I.1
Bujnicki, J.M.2
-
7
-
-
0026572775
-
Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
-
Katchalski-Katzir, E. et al. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A 89, 2195-9 (1992).
-
(1992)
Proc Natl Acad Sci U S A
, vol.89
, pp. 2195-2199
-
-
Katchalski-Katzir, E.1
-
8
-
-
0028575449
-
Hydrophobic docking: A proposed enhancement to molecular recognition techniques
-
Vakser, I. A. & Aflalo, C. Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins 20, 320-9 (1994).
-
(1994)
Proteins
, vol.20
, pp. 320-329
-
-
Vakser, I.A.1
Aflalo, C.2
-
9
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics and biochemical information
-
DOI 10.1006/jmbi.1997.1203
-
Gabb, H. A., Jackson, R. M. & Sternberg, M. J. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 272, 106-20 (1997). (Pubitemid 27395541)
-
(1997)
Journal of Molecular Biology
, vol.272
, Issue.1
, pp. 106-120
-
-
Gabb, H.A.1
Jackson, R.M.2
Sternberg, M.J.E.3
-
10
-
-
0037093643
-
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
-
DOI 10.1002/prot.10092
-
Chen, R. & Weng, Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 47, 281-94 (2002). (Pubitemid 34438678)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.47
, Issue.3
, pp. 281-294
-
-
Chen, R.1
Weng, Z.2
-
11
-
-
0037442962
-
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
-
DOI 10.1021/ja026939x
-
Dominguez, C., Boelens, R. & Bonvin, A. M. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125, 1731-7 (2003). (Pubitemid 36232568)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.7
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.J.J.3
-
12
-
-
79251557484
-
ASPDock: Protein-protein docking algorithm using atomic solvation parameters model
-
Li, L., Guo, D., Huang, Y., Liu, S. & Xiao, Y. ASPDock: protein-protein docking algorithm using atomic solvation parameters model. BMC Bioinformatics 12, 36 (2011).
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 36
-
-
Li, L.1
Guo, D.2
Huang, Y.3
Liu, S.4
Xiao, Y.5
-
13
-
-
0033574510
-
Protein-DNA interactions: A structural analysis
-
DOI 10.1006/jmbi.1999.2659
-
Jones, S., van Heyningen, P., Berman, H. M. & Thornton, J. M. Protein-DNA interactions: A structural analysis. J Mol Biol 287, 877-96 (1999). (Pubitemid 29188875)
-
(1999)
Journal of Molecular Biology
, vol.287
, Issue.5
, pp. 877-896
-
-
Jones, S.1
Van Heyningen, P.2
Berman, H.M.3
Thornton, J.M.4
-
14
-
-
43349105225
-
Dissecting protein-RNA recognition sites
-
DOI 10.1093/nar/gkn102
-
Bahadur, R. P., Zacharias, M. & Janin, J. Dissecting protein-RNA recognition sites. Nucleic Acids Res 36, 2705-16 (2008). (Pubitemid 351659584)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.8
, pp. 2705-2716
-
-
Bahadur, R.P.1
Zacharias, M.2
Janin, J.3
-
15
-
-
84873031500
-
Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials
-
Perez-Cano, L., Solernou, A., Pons, C. & Fernandez-Recio, J. Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials. Pac Symp Biocomput, 293-301 (2010).
-
(2010)
Pac Symp Biocomput
, pp. 293-301
-
-
Perez-Cano, L.1
Solernou, A.2
Pons, C.3
Fernandez-Recio, J.4
-
16
-
-
33746526551
-
Prediction of RNA binding sites in proteins from amino acid sequence
-
DOI 10.1261/rna.2197306
-
Terribilini, M. et al. Prediction of RNA binding sites in proteins from amino acid sequence. RNA 12, 1450-62 (2006). (Pubitemid 44141524)
-
(2006)
RNA
, vol.12
, Issue.8
, pp. 1450-1462
-
-
Terribilini, M.1
Lee, J.-H.2
Yan, C.3
Jernigan, R.L.4
Honavar, V.5
Dobbs, D.6
-
17
-
-
33845865515
-
Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction
-
DOI 10.1093/nar/gkl819
-
Kim, O. T., Yura, K. & Go, N. Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction. Nucleic Acids Res 34, 6450-60 (2006). (Pubitemid 46017942)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.22
, pp. 6450-6460
-
-
Kim, O.T.P.1
Yura, K.2
Go, N.3
-
18
-
-
40549105098
-
Prediction of RNA binding sites in a protein using SVM and PSSM profile
-
DOI 10.1002/prot.21677
-
Kumar, M., Gromiha, M. M. & Raghava, G.P. PredictionofRNA binding sitesin a protein using SVM and PSSM profile. Proteins 71, 189-94 (2008). (Pubitemid 351358602)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.71
, Issue.1
, pp. 189-194
-
-
Kumar, M.1
Gromiha, M.M.2
Raghava, G.P.S.3
-
19
-
-
77949343955
-
Optimal protein-RNA area, OPRA: A propensity-based method to identify RNA-binding sites on proteins
-
Perez-Cano, L. & Fernandez-Recio, J. Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins. Proteins 78, 25-35 (2010).
-
(2010)
Proteins
, vol.78
, pp. 25-35
-
-
Perez-Cano, L.1
Fernandez-Recio, J.2
-
20
-
-
0035800599
-
Structure-based analysis of protein-RNA interactions using the program ENTANGLE
-
DOI 10.1006/jmbi.2001.4857
-
Allers, J. & Shamoo, Y. Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J Mol Biol 311, 75-86 (2001). (Pubitemid 32735315)
-
(2001)
Journal of Molecular Biology
, vol.311
, Issue.1
, pp. 75-86
-
-
Allers, J.1
Shamoo, Y.2
-
21
-
-
84860369519
-
Dissecting the protein-RNA interface: The role of protein surface shapes and RNA secondary structures in protein-RNA recognition
-
Iwakiri, J., Tateishi, H., Chakraborty, A., Patil, P. & Kenmochi, N. Dissecting the protein-RNA interface: the role of protein surface shapes and RNA secondary structures in protein-RNA recognition. Nucleic Acids Res 40, 3299-306 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 3299-3306
-
-
Iwakiri, J.1
Tateishi, H.2
Chakraborty, A.3
Patil, P.4
Kenmochi, N.5
-
22
-
-
79957745800
-
The role of RNA sequence and structure in RNA-protein interactions
-
Gupta, A. & Gribskov, M. The role of RNA sequence and structure in RNA-protein interactions. J Mol Biol 409, 574-87 (2011).
-
(2011)
J Mol Biol
, vol.409
, pp. 574-587
-
-
Gupta, A.1
Gribskov, M.2
-
23
-
-
84862173240
-
Aprotein-RNA docking benchmark (II): Extended set from experimental and homology modeling data
-
Perez-Cano, L., Jimenez-Garcia, B. & Fernandez-Recio, J. Aprotein-RNA docking benchmark (II): extended set from experimental and homology modeling data. Proteins 80, 1872-82 (2012).
-
(2012)
Proteins
, vol.80
, pp. 1872-1882
-
-
Perez-Cano, L.1
Jimenez-Garcia, B.2
Fernandez-Recio, J.3
-
24
-
-
84872598339
-
A nonredundant structure dataset for benchmarking protein-RNA computational docking
-
Huang, S. Y. & Zou, X. A nonredundant structure dataset for benchmarking protein-RNA computational docking. J Comput Chem 34, 311-318 (2013).
-
(2013)
J Comput Chem
, vol.34
, pp. 311-318
-
-
Huang, S.Y.1
Zou, X.2
-
25
-
-
23444454552
-
The Amber biomolecular simulation programs
-
DOI 10.1002/jcc.20290
-
Case, D. A. et al. The Amber biomolecular simulation programs. J Comput Chem 26, 1668-88 (2005). (Pubitemid 43076180)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
26
-
-
79960036791
-
DECK: Distance and environment-dependent, coarsegrained, knowledge-based potentials for protein-protein docking
-
Liu, S. & Vakser, I. A. DECK: Distance and environment-dependent, coarsegrained, knowledge-based potentials for protein-protein docking. BMC Bioinformatics 12, 280 (2011).
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 280
-
-
Liu, S.1
Vakser, I.A.2
-
27
-
-
34248371273
-
Predicting protein-protein interactions based only on sequences information
-
DOI 10.1073/pnas.0607879104
-
Shen, J. et al. Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci U S A 104, 4337-41 (2007). (Pubitemid 47186227)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.11
, pp. 4337-4341
-
-
Shen, J.1
Zhang, J.2
Luo, X.3
Zhu, W.4
Yu, K.5
Chen, K.6
Li, Y.7
Jiang, H.8
-
28
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-637 (1983).
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
29
-
-
0242396923
-
3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
DOI 10.1093/nar/gkg680
-
Lu, X. J. & Olson, W.K.3DNA: asoftware packagefor the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31, 5108-21 (2003). (Pubitemid 37441878)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.17
, pp. 5108-5121
-
-
Lu, X.-J.1
Olson, W.K.2
-
30
-
-
0345059376
-
Announcing the worldwide Protein Data Bank
-
DOI 10.1038/nsb1203-980
-
Berman, H., Henrick, K. & Nakamura, H. Announcing the worldwide Protein Data Bank. Nat Struct Biol 10, 980 (2003). (Pubitemid 37500485)
-
(2003)
Nature Structural Biology
, vol.10
, Issue.12
, pp. 980
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
-
31
-
-
57349132441
-
Protein-protein docking benchmark version 3.0
-
DOI 10.1002/prot.22106
-
Hwang, H., Pierce, B., Mintseris, J., Janin, J. & Weng, Z. Protein-protein docking benchmark version 3.0. Proteins 73, 705-9 (2008). (Pubitemid 352788651)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.73
, Issue.3
, pp. 705-709
-
-
Hwang, H.1
Pierce, B.2
Mintseris, J.3
Janin, J.4
Weng, Z.5
|