-
1
-
-
58149305794
-
An empirical framework for binary interactome mapping
-
Venkatesan,K., Rual,J.F., Vazquez,A., Stelzl,U., Lemmens,I., Hirozane-Kishikawa,T., Hao,T., Zenkner,M., Xin,X., Goh,K.I. et al. (2009) An empirical framework for binary interactome mapping. Nat. Methods, 6, 83-90.
-
(2009)
Nat. Methods
, vol.6
, pp. 83-90
-
-
Venkatesan, K.1
Rual, J.F.2
Vazquez, A.3
Stelzl, U.4
Lemmens, I.5
Hirozane-Kishikawa, T.6
Hao, T.7
Zenkner, M.8
Xin, X.9
Goh, K.I.10
-
2
-
-
44349113144
-
Estimating the size of the human interactome
-
Stumpf,M.P., Thorne,T., de Silva,E., Stewart,R., An,H.J., Lappe,M. and Wiuf,C. (2008) Estimating the size of the human interactome. Proc. Natl. Acad. Sci. U.S.A., 105, 6959-6964.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 6959-6964
-
-
Stumpf, M.P.1
Thorne, T.2
De Silva, E.3
Stewart, R.4
An, H.J.5
Lappe, M.6
Wiuf, C.7
-
3
-
-
84871967106
-
Interactome3D: Adding structural details to protein networks
-
Mosca,R., Ceol,A. and Aloy,P. (2013) Interactome3D: adding structural details to protein networks. Nat. Methods, 10, 47-53.
-
(2013)
Nat. Methods
, vol.10
, pp. 47-53
-
-
Mosca, R.1
Ceol, A.2
Aloy, P.3
-
4
-
-
84857788445
-
Large-scale mapping of human protein interactome using structural complexes
-
Tyagi,M., Hashimoto,K., Shoemaker,B.A., Wuchty,S. and Panchenko,A.R. (2012) Large-scale mapping of human protein interactome using structural complexes. EMBO Rep., 13, 266-271.
-
(2012)
EMBO Rep.
, vol.13
, pp. 266-271
-
-
Tyagi, M.1
Hashimoto, K.2
Shoemaker, B.A.3
Wuchty, S.4
Panchenko, A.R.5
-
5
-
-
84862625522
-
Constructing structural networks of signaling pathways on the proteome scale
-
Kuzu,G., Keskin,O., Gursoy,A. and Nussinov,R. (2012) Constructing structural networks of signaling pathways on the proteome scale. Curr. Opin. Struct. Biol., 22, 367-377.
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 367-377
-
-
Kuzu, G.1
Keskin, O.2
Gursoy, A.3
Nussinov, R.4
-
6
-
-
79960164372
-
Protein-protein complex structure predictions by multimeric threading and template recombination
-
Mukherjee,S. and Zhang,Y. (2011) Protein-protein complex structure predictions by multimeric threading and template recombination. Structure, 19, 955-966.
-
(2011)
Structure
, vol.19
, pp. 955-966
-
-
Mukherjee, S.1
Zhang, Y.2
-
7
-
-
84875464398
-
Mapping monomeric threading to protein-protein structure prediction
-
Guerler,A., Govindarajoo,B. and Zhang,Y. (2013) Mapping monomeric threading to protein-protein structure prediction. J. Chem. Inf. Model., 53, 717-725.
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 717-725
-
-
Guerler, A.1
Govindarajoo, B.2
Zhang, Y.3
-
8
-
-
0037110589
-
MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading
-
Lu,L., Lu,H. and Skolnick,J. (2002) MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins, 49, 350-364.
-
(2002)
Proteins
, vol.49
, pp. 350-364
-
-
Lu, L.1
Lu, H.2
Skolnick, J.3
-
9
-
-
80052411919
-
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
-
Tuncbag,N., Gursoy,A., Nussinov,R. and Keskin,O. (2011) Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat. Protoc., 6, 1341-1354.
-
(2011)
Nat. Protoc.
, vol.6
, pp. 1341-1354
-
-
Tuncbag, N.1
Gursoy, A.2
Nussinov, R.3
Keskin, O.4
-
10
-
-
84857790849
-
Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement
-
Tuncbag,N., Keskin,O., Nussinov,R. and Gursoy,A. (2012) Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. Proteins, 80, 1239-1249.
-
(2012)
Proteins
, vol.80
, pp. 1239-1249
-
-
Tuncbag, N.1
Keskin, O.2
Nussinov, R.3
Gursoy, A.4
-
11
-
-
84879327937
-
Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale
-
Kuzu,G., Gursoy,A., Nussinov,R. and Keskin,O. (2013) Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. J. Proteome Res., 12, 2641-2653.
-
(2013)
J. Proteome Res.
, vol.12
, pp. 2641-2653
-
-
Kuzu, G.1
Gursoy, A.2
Nussinov, R.3
Keskin, O.4
-
12
-
-
84888307602
-
Global and local structural similarity in protein-protein complexes: Implications for template-based docking
-
Kundrotas,P.J. and Vakser,I.A. (2013) Global and local structural similarity in protein-protein complexes: implications for template-based docking. Proteins, 81, 2137-2142.
-
(2013)
Proteins
, vol.81
, pp. 2137-2142
-
-
Kundrotas, P.J.1
Vakser, I.A.2
-
13
-
-
20844454090
-
Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces
-
Aytuna,A.S., Gursoy,A. and Keskin,O. (2005) Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics, 21, 2850-2855.
-
(2005)
Bioinformatics
, vol.21
, pp. 2850-2855
-
-
Aytuna, A.S.1
Gursoy, A.2
Keskin, O.3
-
14
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan,A.A. and Thorn,K.S. (1998) Anatomy of hot spots in protein interfaces. J. Mol. Biol., 280, 1-9.
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 1-9
-
-
Bogan, A.A.1
Thorn, K.S.2
-
15
-
-
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
-
16
-
-
0033954256
-
The protein data bank
-
Berman,H.M.,Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,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
Bourne, P.E.8
-
17
-
-
23144463510
-
PRISM: Protein interactions by structural matching
-
Ogmen,U., Keskin,O., Aytuna,A.S., Nussinov,R. and Gursoy,A. (2005) PRISM: protein interactions by structural matching. Nucleic Acids Res., 33, W331-W336.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Ogmen, U.1
Keskin, O.2
Aytuna, A.S.3
Nussinov, R.4
Gursoy, A.5
-
18
-
-
77951232176
-
FiberDock: Flexible induced-fit backbone refinement in molecular docking
-
Mashiach,E., Nussinov,R. and Wolfson,H.J. (2010) FiberDock: flexible induced-fit backbone refinement in molecular docking. Proteins, 78, 1503-1519.
-
(2010)
Proteins
, vol.78
, pp. 1503-1519
-
-
Mashiach, E.1
Nussinov, R.2
Wolfson, H.J.3
-
19
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell,A.D., Bashford,D., Bellott,M., Dunbrack,R.L., Evanseck,J.D., Field,M.J., Fischer,S., Gao,J., Guo,H., Ha,S. et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
-
20
-
-
84900297215
-
Non-redundant unique interface structures as templates for modeling protein interactions
-
Cukuroglu,E., Gursoy,A., Nussinov,R. and Keskin,O. (2014) Non-redundant unique interface structures as templates for modeling protein interactions. PLoS One, 9, e86738.
-
(2014)
PLoS One
, vol.9
-
-
Cukuroglu, E.1
Gursoy, A.2
Nussinov, R.3
Keskin, O.4
-
21
-
-
84861036418
-
HotRegion: A database of predicted hot spot clusters
-
Cukuroglu,E., Gursoy,A. and Keskin,O. (2012) HotRegion: a database of predicted hot spot clusters. Nucleic Acids Res., 40, D829-D833.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Cukuroglu, E.1
Gursoy, A.2
Keskin, O.3
-
22
-
-
66349094681
-
Identification of computational hot spots in protein interfaces: Combining solvent accessibility and inter-residue potentials improves the accuracy
-
Tuncbag,N., Gursoy,A. and Keskin,O. (2009) Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics, 25, 1513-1520.
-
(2009)
Bioinformatics
, vol.25
, pp. 1513-1520
-
-
Tuncbag, N.1
Gursoy, A.2
Keskin, O.3
-
23
-
-
0003742069
-
-
Department ofBiochemistry and Molecular Biology, University College London
-
Hubbard S.J. and Thornton,J.M. (1993) 'NACCESS', Computer Program. Department ofBiochemistry and Molecular Biology, University College London5
-
(1993)
'NACCESS', Computer Program
, vol.5
-
-
Hubbard, S.J.1
Thornton, J.M.2
-
24
-
-
2442456104
-
A method for simultaneous alignment of multiple protein structures
-
Shatsky,M., Nussinov,R. and Wolfson,H.J. (2004) A method for simultaneous alignment of multiple protein structures. Proteins, 56, 143-156.
-
(2004)
Proteins
, vol.56
, pp. 143-156
-
-
Shatsky, M.1
Nussinov, R.2
Wolfson, H.J.3
-
25
-
-
84876239078
-
JSmol and the next-generation web-based representation of 3D molecular structure as applied to proteopedia
-
Hanson,R.M., Prilusky,J., Renjian,Z., Nakane,T. and Sussman,J.L. (2013) JSmol and the next-generation web-based representation of 3D molecular structure as applied to proteopedia. Isr. J. Chem., 53, 207-216
-
(2013)
Isr. J. Chem.
, vol.53
, pp. 207-216
-
-
Hanson, R.M.1
Prilusky, J.2
Renjian, Z.3
Nakane, T.4
Sussman, J.L.5
|