-
1
-
-
84921721617
-
Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins
-
Kramer, K., Sachsenberg, T., Beckmann, B.M., Qamar, S., Boon, K.-L., Hentze, M.W., Kohlbacher, O. and Urlaub, H. (2014) Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nat. Methods, 11, 1064-1070.
-
(2014)
Nat. Methods
, vol.11
, pp. 1064-1070
-
-
Kramer, K.1
Sachsenberg, T.2
Beckmann, B.M.3
Qamar, S.4
Boon, K.-L.5
Hentze, M.W.6
Kohlbacher, O.7
Urlaub, H.8
-
2
-
-
84920519673
-
Oming in on RNA-protein interactions
-
Rinn, J.L. and Ule, J. (2014) 'Oming in on RNA-protein interactions. Genome Biol., 15, 401.
-
(2014)
Genome Biol.
, vol.15
, pp. 401
-
-
Rinn, J.L.1
Ule, J.2
-
3
-
-
84883319580
-
Prediction of RNA binding proteins comes of age from low resolution to high resolution
-
Zhao, H.Y., Yang, Y.D. and Zhou, Y.Q. (2013) Prediction of RNA binding proteins comes of age from low resolution to high resolution. Mol. Biosyst., 9, 2417-2425.
-
(2013)
Mol. Biosyst.
, vol.9
, pp. 2417-2425
-
-
Zhao, H.Y.1
Yang, Y.D.2
Zhou, Y.Q.3
-
4
-
-
84865194573
-
Computational methods for prediction of protein-RNA interactions
-
Puton, T., Kozlowski, L., Tuszynska, I., Rother, K. and Bujnicki, J.M. (2012) Computational methods for prediction of protein-RNA interactions. J. Struct. Biol., 179, 261-268.
-
(2012)
J. Struct. Biol.
, vol.179
, pp. 261-268
-
-
Puton, T.1
Kozlowski, L.2
Tuszynska, I.3
Rother, K.4
Bujnicki, J.M.5
-
5
-
-
77953886400
-
BindN plus for accurate prediction of DNA and RNA-binding residues from protein sequence features
-
Wang, L.J., Huang, C.Y., Yang, M.Q. and Yang, J.Y. (2010) BindN plus for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst. Biol., 4(Suppl. 1), S3.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. S3
-
-
Wang, L.J.1
Huang, C.Y.2
Yang, M.Q.3
Yang, J.Y.4
-
6
-
-
84901298266
-
RNABindRPlus: A predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins
-
Walia, R.R., Xue, L.C., Wilkins, K., El-Manzalawy, Y., Dobbs, D. and Honavar, V. (2014) RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins. PLoS One, 9, e97725.
-
(2014)
PLoS One
, vol.9
, pp. e97725
-
-
Walia, R.R.1
Xue, L.C.2
Wilkins, K.3
El-Manzalawy, Y.4
Dobbs, D.5
Honavar, V.6
-
7
-
-
34547573759
-
Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces
-
Shazman, S., Celniker, G., Haber, O., Glaser, F. and Mandel-Gutfreund, Y. (2007) Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces. Nucleic Acids Res., 35, W526-W530.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. W526-W530
-
-
Shazman, S.1
Celniker, G.2
Haber, O.3
Glaser, F.4
Mandel-Gutfreund, Y.5
-
8
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker, N.A., Sept, D., Joseph, S., Holst, M.J. and McCammon, J.A. (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. U.S.A., 98, 10037-10041.
-
(2001)
Proc. Natl Acad. Sci. U.S.A.
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
9
-
-
84876210821
-
ConSurf: Using evolutionary data to raise testable hypotheses about protein function
-
Celniker, G., Nimrod, G., Ashkenazy, H., Glaser, F., Martz, E., Mayrose, I., Pupko, T. and Ben-Tal, N. (2013) ConSurf: using evolutionary data to raise testable hypotheses about protein function. Isr. J. Chem., 53, 199-206.
-
(2013)
Isr. J. Chem.
, vol.53
, pp. 199-206
-
-
Celniker, G.1
Nimrod, G.2
Ashkenazy, H.3
Glaser, F.4
Martz, E.5
Mayrose, I.6
Pupko, T.7
Ben-Tal, N.8
-
10
-
-
84899099295
-
Prediction of RNA binding residues: An extensive analysis based on structure and function to select the best predictor
-
Nagarajan, R. and Gromiha, M.M. (2014) Prediction of RNA binding residues: an extensive analysis based on structure and function to select the best predictor. PLoS One, 9, e91140.
-
(2014)
PLoS One
, vol.9
, pp. e91140
-
-
Nagarajan, R.1
Gromiha, M.M.2
-
11
-
-
77954247239
-
NAPS: A residue-level nucleic acid-binding prediction server
-
Carson, M.B., Langlois, R. and Lu, H. (2010) NAPS: a residue-level nucleic acid-binding prediction server. Nucleic Acids Res., 38, W431-W435.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W431-W435
-
-
Carson, M.B.1
Langlois, R.2
Lu, H.3
-
12
-
-
33747828217
-
BindN: A web-based tool for effcient prediction of DNA and RNA binding sites in amino acid sequences
-
Wang, L.J. and Brown, S.J. (2006) BindN: a web-based tool for effcient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res., 34, W243-W248.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. W243-W248
-
-
Wang, L.J.1
Brown, S.J.2
-
13
-
-
84876514881
-
NPIDB: Nucleic acid-protein interaction database
-
Kirsanov, D.D., Zanegina, O.N., Aksianov, E.A., Spirin, S.A., Karyagina, A.S. and Alexeevski, A.V. (2013) NPIDB: nucleic acid-protein interaction database. Nucleic Acids Res., 41, D517-D523.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D517-D523
-
-
Kirsanov, D.D.1
Zanegina, O.N.2
Aksianov, E.A.3
Spirin, S.A.4
Karyagina, A.S.5
Alexeevski, A.V.6
-
14
-
-
0043180474
-
PISCES: A protein sequence culling server
-
Wang, G.L. and Dunbrack, R.L. (2003) PISCES: a protein sequence culling server. Bioinformatics, 19, 1589-1591.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.L.1
Dunbrack, R.L.2
-
15
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
Zhang, Y. and Skolnick, J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302-2309.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
16
-
-
40549105098
-
Prediction of RNA binding sites in a protein using SVM and PSSM profle
-
Kumar, M., Gromiha, A.M. and Raghava, G.P.S. (2008) Prediction of RNA binding sites in a protein using SVM and PSSM profle. Proteins, 71, 189-194.
-
(2008)
Proteins
, vol.71
, pp. 189-194
-
-
Kumar, M.1
Gromiha, A.M.2
Raghava, G.P.S.3
-
17
-
-
33746526551
-
Prediction of RNA binding sites in proteins from amino acid sequence
-
Terribilini, M., Lee, J.H., Yan, C.H., Jernigan, R.L., Honavar, V. and Dobbs, D. (2006) Prediction of RNA binding sites in proteins from amino acid sequence. RNA, 12, 1450-1462.
-
(2006)
RNA
, vol.12
, pp. 1450-1462
-
-
Terribilini, M.1
Lee, J.H.2
Yan, C.H.3
Jernigan, R.L.4
Honavar, V.5
Dobbs, D.6
-
18
-
-
34547560560
-
RNABindR: A server for analyzing and predicting RNA-binding sites in proteins
-
Terribilini, M., Sander, J.D., Lee, J.H., Zaback, P., Jernigan, R.L., Honavar, V. and Dobbs, D. (2007) RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res., 35, W578-W584.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. W578-W584
-
-
Terribilini, M.1
Sander, J.D.2
Lee, J.H.3
Zaback, P.4
Jernigan, R.L.5
Honavar, V.6
Dobbs, D.7
-
19
-
-
84929652993
-
Quantifying sequence and structural features of protein-RNA interactions
-
Li, S., Yamashita, K., Amada, K.M. and Standley, D.M. (2014) Quantifying sequence and structural features of protein-RNA interactions. Nucleic Acids Res., 42, 10086-10098.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 10086-10098
-
-
Li, S.1
Yamashita, K.2
Amada, K.M.3
Standley, D.M.4
-
20
-
-
84871869026
-
Prediction of RNA-binding amino acids from protein and RNA sequences
-
Choi, S. and Han, K. (2011) Prediction of RNA-binding amino acids from protein and RNA sequences. BMC Bioinform., 12(Suppl. 13), S7.
-
(2011)
BMC Bioinform.
, vol.12
, pp. S7
-
-
Choi, S.1
Han, K.2
-
21
-
-
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
-
22
-
-
0346258292
-
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
-
Jones, S., Shanahan, H.P., Berman, H.M. and Thornton, J.M. (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res., 31, 7189-7198.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 7189-7198
-
-
Jones, S.1
Shanahan, H.P.2
Berman, H.M.3
Thornton, J.M.4
-
23
-
-
58049220320
-
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
-
Wu, J.S., Liu, H.D., Duan, X.Y., Ding, Y., Wu, H.T., Bai, Y.F. and Sun, X. (2009) Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics, 25, 30-35.
-
(2009)
Bioinformatics
, vol.25
, pp. 30-35
-
-
Wu, J.S.1
Liu, H.D.2
Duan, X.Y.3
Ding, Y.4
Wu, H.T.5
Bai, Y.F.6
Sun, X.7
-
24
-
-
33846803179
-
DISPLAR: An accurate method for predicting DNA-binding sites on protein surfaces
-
Tjong, H. and Zhou, H.X. (2007) DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Res., 35, 1465-1477.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 1465-1477
-
-
Tjong, H.1
Zhou, H.X.2
-
25
-
-
77954297726
-
DNABINDPROT: Fuctuation-based predictor of DNA-binding residues within a network of interacting residues
-
Ozbek, P., Soner, S., Erman, B. and Haliloglu, T. (2010) DNABINDPROT: fuctuation-based predictor of DNA-binding residues within a network of interacting residues. Nucleic Acids Res., 38, W417-W423.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W417-W423
-
-
Ozbek, P.1
Soner, S.2
Erman, B.3
Haliloglu, T.4
-
26
-
-
84875182078
-
PreDNA: Accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information
-
Li, T., Li, Q.Z., Liu, S., Fan, G.L., Zuo, Y.C. and Peng, Y. (2013) PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information. Bioinformatics, 29, 678-685.
-
(2013)
Bioinformatics
, vol.29
, pp. 678-685
-
-
Li, T.1
Li, Q.Z.2
Liu, S.3
Fan, G.L.4
Zuo, Y.C.5
Peng, Y.6
-
27
-
-
79959217445
-
MetaDBSite: A meta approach to improve protein DNA-binding sites prediction
-
Si, J.N., Zhang, Z.M., Lin, B.Y., Schroeder, M. and Huang, B.D. (2011) MetaDBSite: a meta approach to improve protein DNA-binding sites prediction. BMC Syst. Biol., 5(Suppl. 1), S7.
-
(2011)
BMC Syst. Biol.
, vol.5
, pp. S7
-
-
Si, J.N.1
Zhang, Z.M.2
Lin, B.Y.3
Schroeder, M.4
Huang, B.D.5
-
28
-
-
67649337519
-
Prediction of mono-and di-nucleotide-specifc DNA-binding sites in proteins using neural networks
-
Andrabi, M., Mizuguchi, K., Sarai, A. and Ahmad, S. (2009) Prediction of mono-and di-nucleotide-specifc DNA-binding sites in proteins using neural networks. BMC Struct. Biol., 9, 30.
-
(2009)
BMC Struct. Biol.
, vol.9
, pp. 30
-
-
Andrabi, M.1
Mizuguchi, K.2
Sarai, A.3
Ahmad, S.4
-
29
-
-
77954185426
-
Prediction of protein-RNA binding sites by a random forest method with combined features
-
Liu, Z.P., Wu, L.Y., Wang, Y., Zhang, X.S. and Chen, L.N. (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
-
30
-
-
79952487629
-
Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature
-
Ma, X., Guo, J., Wu, J.S., Liu, H.D., Yu, J.F., Xie, J.M. and Sun, X.A. (2011) Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature. Proteins, 79, 1230-1239.
-
(2011)
Proteins
, vol.79
, pp. 1230-1239
-
-
Ma, X.1
Guo, J.2
Wu, J.S.3
Liu, H.D.4
Yu, J.F.5
Xie, J.M.6
Sun, X.A.7
-
31
-
-
0028304962
-
Satisfying hydrogen-bonding potential in proteins
-
Mcdonald, I.K. and Thornton, J.M. (1994) Satisfying hydrogen-bonding potential in proteins. J. Mol. Biol., 238, 777-793.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
32
-
-
0031191630
-
The use of the area under the roc curve in the evaluation of machine learning algorithms
-
Bradley, A.P. (1997) The use of the area under the roc curve in the evaluation of machine learning algorithms. Pattern Recogn., 30, 1145-1159.
-
(1997)
Pattern Recogn.
, vol.30
, pp. 1145-1159
-
-
Bradley, A.P.1
-
33
-
-
0017429069
-
Areas, volumes, packing, and protein structure
-
Richards, F.M. (1977) Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng., 6, 151-176.
-
(1977)
Annu. Rev. Biophys. Bioeng.
, vol.6
, pp. 151-176
-
-
Richards, F.M.1
-
34
-
-
34547559704
-
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
Dolinsky, T.J., Czodrowski, P., Li, H., Nielsen, J.E., Jensen, J.H., Klebe, G. and Baker, N.A. (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res., 35, W522-W525.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. W522-W525
-
-
Dolinsky, T.J.1
Czodrowski, P.2
Li, H.3
Nielsen, J.E.4
Jensen, J.H.5
Klebe, G.6
Baker, N.A.7
-
35
-
-
3242886771
-
PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
Dolinsky, T.J., Nielsen, J.E., McCammon, J.A. and Baker, N.A. (2004) PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res., 32, W665-W667.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. W665-W667
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
36
-
-
84856489442
-
HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment
-
Remmert, M., Biegert, A., Hauser, A. and Soding, J. (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods, 9, 173-175.
-
(2012)
Nat. Methods
, vol.9
, pp. 173-175
-
-
Remmert, M.1
Biegert, A.2
Hauser, A.3
Soding, J.4
-
37
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks, G., Hon, G., Chandonia, J.-M. and Brenner, S. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188-1190.
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.1
Hon, G.2
Chandonia, J.-M.3
Brenner, S.4
-
38
-
-
84940644968
-
A mathematical theory of communication
-
Shannon, C.E. (1948) A mathematical theory of communication. Bell Syst. Tech. J., 27, 379-423.
-
(1948)
Bell Syst. Tech. J.
, vol.27
, pp. 379-423
-
-
Shannon, C.E.1
-
39
-
-
50949129815
-
Classifying RNA-binding proteins based on electrostatic properties
-
Shazman, S. and Mandel-Gutfreund, Y. (2008) Classifying RNA-binding proteins based on electrostatic properties. PloS Comput. Biol., 4, e1000146.
-
(2008)
PloS Comput. Biol.
, vol.4
, pp. e1000146
-
-
Shazman, S.1
Mandel-Gutfreund, Y.2
-
40
-
-
33746495377
-
Predicting DNA-binding sites of proteins from amino acid sequence
-
Yan, C.H., Terribilini, M., Wu, F.H., Jernigan, R.L., Dobbs, D. and Honavar, V. (2006) Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinform., 7, 262.
-
(2006)
BMC Bioinform.
, vol.7
, pp. 262
-
-
Yan, C.H.1
Terribilini, M.2
Wu, F.H.3
Jernigan, R.L.4
Dobbs, D.5
Honavar, V.6
-
41
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J.H., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.H.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
42
-
-
0029916911
-
The SWISS-PROT protein sequence data bank and its new supplement TREMBL
-
Bairoch, A. and Apweiler, R. (1996) The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res., 24, 21-25.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 21-25
-
-
Bairoch, A.1
Apweiler, R.2
-
44
-
-
85019427531
-
Comparative protein structure modeling using MODELLER
-
Eswar, N., Webb, B., Marti-Renom, M.A., Madhusudhan, M.S., Eramian, D., Shen, M.Y., Pieper, U. and Sali, A. (2007) Comparative protein structure modeling using MODELLER. Curr. Protoc. Protein Sci., 50, 2.9.1-2.9.31.
-
(2007)
Curr. Protoc. Protein Sci.
, vol.50
, pp. 291-2931
-
-
Eswar, N.1
Webb, B.2
Marti-Renom, M.A.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.Y.6
Pieper, U.7
Sali, A.8
-
45
-
-
79351468726
-
Analysis of electric moments of RNA-binding proteins: Implications for mechanism and prediction
-
Ahmad, S. and Sarai, A. (2011) Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction. BMC Struct. Biol., 11, 8.
-
(2011)
BMC Struct. Biol.
, vol.11
, pp. 8
-
-
Ahmad, S.1
Sarai, A.2
-
46
-
-
41149087805
-
Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry
-
Chen, Y.C. and Lim, C. (2008) Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res., 36, e29.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. e29
-
-
Chen, Y.C.1
Lim, C.2
-
47
-
-
79955638463
-
Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets
-
Zhao, H.Y., Yang, Y.D. and Zhou, Y.Q. (2011) Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res., 39, 3017-3025.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 3017-3025
-
-
Zhao, H.Y.1
Yang, Y.D.2
Zhou, Y.Q.3
-
48
-
-
77949343955
-
Optimal protein-RNA area, OPRA: A propensity-based method to identify RNA-binding sites on proteins
-
Perez-Cano, L. and Fernandez-Recio, J. (2010) Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins. Proteins, 78, 25-35.
-
(2010)
Proteins
, vol.78
, pp. 25-35
-
-
Perez-Cano, L.1
Fernandez-Recio, J.2
-
49
-
-
84872598339
-
A nonredundant structure dataset for benchmarking protein-RNA computational docking
-
Huang, S.Y. and Zou, X. (2013) A nonredundant structure dataset for benchmarking protein-RNA computational docking. J. Comput. Chem., 34, 311-318.
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 311-318
-
-
Huang, S.Y.1
Zou, X.2
-
50
-
-
84862163178
-
A protein-RNA docking benchmark (I): Nonredundant cases
-
Barik, A., C, N., P, M. and Bahadur, R.P. (2012) A protein-RNA docking benchmark (I): nonredundant cases. Proteins, 80, 1866-1871.
-
(2012)
Proteins
, vol.80
, pp. 1866-1871
-
-
Barik, A.C.N.P.M.1
Bahadur, R.P.2
-
51
-
-
84862173240
-
A protein-RNA docking benchmark (II): Extended set from experimental and homology modeling data
-
Perez-Cano, L., Jimenez-Garcia, B. and Fernandez-Recio, J. (2012) A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data. Proteins, 80, 1872-1882.
-
(2012)
Proteins
, vol.80
, pp. 1872-1882
-
-
Perez-Cano, L.1
Jimenez-Garcia, B.2
Fernandez-Recio, J.3
-
52
-
-
47249125424
-
DBD-Hunter: A knowledge-based method for the prediction of DNA-protein interactions
-
Gao, M. and Skolnick, J. (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res., 36, 3978-3992.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 3978-3992
-
-
Gao, M.1
Skolnick, J.2
-
54
-
-
33845865515
-
Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction
-
Kim, O.T.P., Yura, K. and Go, N. (2006) Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction. Nucleic Acids Res., 34, 6450-6460.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 6450-6460
-
-
Kim, O.T.P.1
Yura, K.2
Go, N.3
-
55
-
-
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 Bioinform., 6, 33.
-
(2005)
BMC Bioinform.
, vol.6
, pp. 33
-
-
Ahmad, S.1
Sarai, A.2
-
56
-
-
84929116149
-
Cross-validation under separate sampling: Strong bias and how to correct it
-
Braga-Neto, U.M., Zollanvari, A. and Dougherty, E.R. (2014) Cross-validation under separate sampling: strong bias and how to correct it. Bioinformatics, 30, 3349-3355.
-
(2014)
Bioinformatics
, vol.30
, pp. 3349-3355
-
-
Braga-Neto, U.M.1
Zollanvari, A.2
Dougherty, E.R.3
-
57
-
-
0034823943
-
Statistical analysis of atomic contacts at RNA-protein interfaces
-
Treger, M. and Westhof, E. (2001) Statistical analysis of atomic contacts at RNA-protein interfaces. J. Mol. Recognit., 14, 199-214.
-
(2001)
J. Mol. Recognit.
, vol.14
, pp. 199-214
-
-
Treger, M.1
Westhof, E.2
-
58
-
-
0035022941
-
Intrinsically disordered protein
-
Dunker, A.K., Lawson, J.D., Brown, C.J., Williams, R.M., Romero, P., Oh, J.S., Oldfeld, C.J., Campen, A.M., Ratliff, C.R., Hipps, K.W. et al. (2001) Intrinsically disordered protein. J. Mol. Graph. Model., 19, 26-59.
-
(2001)
J. Mol. Graph. Model.
, vol.19
, pp. 26-59
-
-
Dunker, A.K.1
Lawson, J.D.2
Brown, C.J.3
Williams, R.M.4
Romero, P.5
Oh, J.S.6
Oldfeld, C.J.7
Campen, A.M.8
Ratliff, C.R.9
Hipps, K.W.10
-
59
-
-
84872154756
-
Interactive web-based pointillist visualization of hydrogenic orbitals using Jmol
-
Tully, S.P., Stitt, T.M., Caldwell, R.D., Hardock, B.J., Hanson, R.M. and Maslak, P. (2013) Interactive web-based pointillist visualization of hydrogenic orbitals using Jmol. J. Chem. Educ., 90, 129-131.
-
(2013)
J. Chem. Educ.
, vol.90
, pp. 129-131
-
-
Tully, S.P.1
Stitt, T.M.2
Caldwell, R.D.3
Hardock, B.J.4
Hanson, R.M.5
Maslak, P.6
-
60
-
-
77954257799
-
ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
-
Ashkenazy, H., Erez, E., Martz, E., Pupko, T. and Ben-Tal, N. (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res., 38, W529-W533.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W529-W533
-
-
Ashkenazy, H.1
Erez, E.2
Martz, E.3
Pupko, T.4
Ben-Tal, N.5
-
61
-
-
84860696343
-
Protein-RNA interface residue prediction using machine learning: An assessment of the state of the art
-
Walia, R.R., Caragea, C., Lewis, B.A., Towfc, F., Terribilini, M., El-Manzalawy, Y., Dobbs, D. and Honavar, V. (2012) Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. BMC Bioinform., 13, 89.
-
(2012)
BMC Bioinform.
, vol.13
, pp. 89
-
-
Walia, R.R.1
Caragea, C.2
Lewis, B.A.3
Towfc, F.4
Terribilini, M.5
El-Manzalawy, Y.6
Dobbs, D.7
Honavar, V.8
-
62
-
-
34249316905
-
RNA-binding proteins: Modular design for effcient function
-
Lunde, B.M., Moore, C. and Varani, G. (2007) RNA-binding proteins: modular design for effcient function. Nat. Rev. Mol. Cell Biol., 8, 479-490.
-
(2007)
Nat. Rev. Mol. Cell Biol.
, vol.8
, pp. 479-490
-
-
Lunde, B.M.1
Moore, C.2
Varani, G.3
-
63
-
-
84887419464
-
Promiscuous RNA binding by Polycomb repressive complex 2
-
Davidovich, C., Zheng, L., Goodrich, K.J. and Cech, T.R. (2013) Promiscuous RNA binding by Polycomb repressive complex 2. Nat. Struct. Mol. Biol., 20, 1250-1257.
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 1250-1257
-
-
Davidovich, C.1
Zheng, L.2
Goodrich, K.J.3
Cech, T.R.4
-
64
-
-
84861969926
-
Insights into RNA biology from an atlas of mammalian mRNA-binding proteins
-
Castello, A., Fischer, B., Eichelbaum, K., Horos, R., Beckmann, B.M., Strein, C., Davey, N.E., Humphreys, D.T., Preiss, T., Steinmetz, L.M. et al. (2012) Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell, 149, 1393-1406.
-
(2012)
Cell
, vol.149
, pp. 1393-1406
-
-
Castello, A.1
Fischer, B.2
Eichelbaum, K.3
Horos, R.4
Beckmann, B.M.5
Strein, C.6
Davey, N.E.7
Humphreys, D.T.8
Preiss, T.9
Steinmetz, L.M.10
-
65
-
-
0028209999
-
Enzymes as RNA-binding proteins: A role for (di)nucleotide-binding domains?
-
Hentze, M.W. (1994) Enzymes as RNA-binding proteins: a role for (di)nucleotide-binding domains? Trends Biochem. Sci., 19, 101-103.
-
(1994)
Trends Biochem. Sci.
, vol.19
, pp. 101-103
-
-
Hentze, M.W.1
|