-
1
-
-
35748953417
-
Structural genomics: Winning the second half of the game
-
Janin J. 2007. Structural genomics: Winning the second half of the game. Structure 15(11):1347-1349.
-
(2007)
Structure
, vol.15
, Issue.11
, pp. 1347-1349
-
-
Janin, J.1
-
2
-
-
37549063951
-
PSI has to live and become PCI: Protein Complex Initiative
-
Vakser IA. 2008. PSI has to live and become PCI: Protein Complex Initiative. Structure 16(1):1-3.
-
(2008)
Structure
, vol.16
, Issue.1
, pp. 1-3
-
-
Vakser, I.A.1
-
3
-
-
34447286664
-
Trp/Met/Phe hot spots in protein-protein interactions: Potential targets in drug design
-
Ma B, Nussinov R. 2007. Trp/Met/Phe hot spots in protein-protein interactions: Potential targets in drug design. Curr Top Med Chem 7(10):999-1005.
-
(2007)
Curr Top Med Chem
, vol.7
, Issue.10
, pp. 999-1005
-
-
Ma, B.1
Nussinov, R.2
-
4
-
-
46449113031
-
Similar chemistry, but different bond pReferences in inter- versus intra-protein interactions
-
Cohen M, Reichmann D, Neuvirth H, Schreiber G. 2008. Similar chemistry, but different bond pReferences in inter- versus intra-protein interactions. Proteins 72(2):741-753.
-
(2008)
Proteins
, vol.72
, Issue.2
, pp. 741-753
-
-
Cohen, M.1
Reichmann, D.2
Neuvirth, H.3
Schreiber, G.4
-
5
-
-
33847795359
-
Intrinsic disorder and functional proteomics
-
Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, Uversky VN, Dunker AK. 2007. Intrinsic disorder and functional proteomics. Biophys J 92(5):1439-1456.
-
(2007)
Biophys J
, vol.92
, Issue.5
, pp. 1439-1456
-
-
Radivojac, P.1
Iakoucheva, L.M.2
Oldfield, C.J.3
Obradovic, Z.4
Uversky, V.N.5
Dunker, A.K.6
-
6
-
-
34249930159
-
Single-molecule experiments in vitro and in silico
-
Sotomayor M, Schulten K. 2007. Single-molecule experiments in vitro and in silico. Science 316(5828):1144-1148.
-
(2007)
Science
, vol.316
, Issue.5828
, pp. 1144-1148
-
-
Sotomayor, M.1
Schulten, K.2
-
7
-
-
33646839120
-
Characterization of protein-ligand interaction sites using experimental and computational methods
-
Vajda S, Guarnieri F. 2006. Characterization of protein-ligand interaction sites using experimental and computational methods. Curr Opin Drug Discov Devel 9(3):354-362.
-
(2006)
Curr Opin Drug Discov Devel
, vol.9
, Issue.3
, pp. 354-362
-
-
Vajda, S.1
Guarnieri, F.2
-
8
-
-
41949102408
-
Predicting 3D structures of protein-protein complexes
-
Vakser IA, Kundrotas P. 2008. Predicting 3D structures of protein-protein complexes. Curr Pharm Biotechnol 9(2):57-66.
-
(2008)
Curr Pharm Biotechnol
, vol.9
, Issue.2
, pp. 57-66
-
-
Vakser, I.A.1
Kundrotas, P.2
-
10
-
-
37548998973
-
Comparative modeling in structural genomics
-
Moult J. 2008. Comparative modeling in structural genomics. Structure 16(1):14-16.
-
(2008)
Structure
, vol.16
, Issue.1
, pp. 14-16
-
-
Moult, J.1
-
11
-
-
10844235653
-
Optimal docking area: A new method for predicting protein-protein interaction sites
-
Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. 2005. Optimal docking area: A new method for predicting protein-protein interaction sites. Proteins 58(1):134-143.
-
(2005)
Proteins
, vol.58
, Issue.1
, pp. 134-143
-
-
Fernandez-Recio, J.1
Totrov, M.2
Skorodumov, C.3
Abagyan, R.4
-
12
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein Data Bank. Nucleic Acids Res 28(1):235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, 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
-
13
-
-
0036149480
-
Soft protein-protein docking in internal coordinates
-
Fernández-Recio J, Totrov M, Abagyan R. 2002. Soft protein-protein docking in internal coordinates. Protein Sci 11(2):280-291.
-
(2002)
Protein Sci
, vol.11
, Issue.2
, pp. 280-291
-
-
Fernández-Recio, J.1
Totrov, M.2
Abagyan, R.3
-
14
-
-
57349132441
-
Protein-protein docking benchmark version 3. 0
-
Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. 2008. Protein-protein docking benchmark version 3. 0. Proteins 73(3):705-709.
-
(2008)
Proteins
, vol.73
, Issue.3
, pp. 705-709
-
-
Hwang, H.1
Pierce, B.2
Mintseris, J.3
Janin, J.4
Weng, Z.5
-
15
-
-
36749060694
-
DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking
-
Gao Y, Douguet D, Tovchigrechko A, Vakser IA. 2007. DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking. Proteins 69(4):845-851.
-
(2007)
Proteins
, vol.69
, Issue.4
, pp. 845-851
-
-
Gao, Y.1
Douguet, D.2
Tovchigrechko, A.3
Vakser, I.A.4
-
16
-
-
19544390737
-
REVCOM: A robust Bayesian method for evolutionary rate estimation
-
Bordner AJ, Abagyan R. 2005. REVCOM: A robust Bayesian method for evolutionary rate estimation. Bioinformatics 21(10):2315-2321.
-
(2005)
Bioinformatics
, vol.21
, Issue.10
, pp. 2315-2321
-
-
Bordner, A.J.1
Abagyan, R.2
-
17
-
-
3843091516
-
Anchor residues in protein-protein interactions
-
Rajamani D, Thiel S, Vajda S, Camacho CJ. 2004. Anchor residues in protein-protein interactions. Proc Natl Acad Sci USA 101(31):11287-11292.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.31
, pp. 11287-11292
-
-
Rajamani, D.1
Thiel, S.2
Vajda, S.3
Camacho, C.J.4
-
18
-
-
15244355250
-
The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
-
Smith GR, Sternberg MJ, Bates PA. 2005. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol 347(5):1077-1101.
-
(2005)
J Mol Biol
, vol.347
, Issue.5
, pp. 1077-1101
-
-
Smith, G.R.1
Sternberg, M.J.2
Bates, P.A.3
-
19
-
-
0034665713
-
Structural mechanism for STI-571 inhibition of abelson tyrosine kinase
-
Schindler T, Bornmann W, Pellicena P, Miller WT, Clarkson B, Kuriyan J. 2000. Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science 289(5486):1938-1942.
-
(2000)
Science
, vol.289
, Issue.5486
, pp. 1938-1942
-
-
Schindler, T.1
Bornmann, W.2
Pellicena, P.3
Miller, W.T.4
Clarkson, B.5
Kuriyan, J.6
-
20
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O, Bourne HR, Cohen FE. 1996. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257(2):342-358.
-
(1996)
J Mol Biol
, vol.257
, Issue.2
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
21
-
-
2942553723
-
Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking
-
Halperin I, Wolfson H, Nussinov R. 2004. Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure (Camb) 12(6):1027-1038.
-
(2004)
Structure (Camb)
, vol.12
, Issue.6
, pp. 1027-1038
-
-
Halperin, I.1
Wolfson, H.2
Nussinov, R.3
-
22
-
-
0037609791
-
Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
-
Ma B, Elkayam T, Wolfson H, Nussinov R. 2003. Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci USA 100(10):5772-5777.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.10
, pp. 5772-5777
-
-
Ma, B.1
Elkayam, T.2
Wolfson, H.3
Nussinov, R.4
-
23
-
-
0037265213
-
Prediction of protein-protein interactions from evolutionary information
-
Valencia A, Pazos F. 2003. Prediction of protein-protein interactions from evolutionary information. Methods Biochem Anal 44:411-426.
-
(2003)
Methods Biochem Anal
, vol.44
, pp. 411-426
-
-
Valencia, A.1
Pazos, F.2
-
24
-
-
0036468670
-
Evolutionary predictions of binding surfaces and interactions
-
Lichtarge O, Sowa ME. 2002. Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol 12(1):21-27.
-
(2002)
Curr Opin Struct Biol
, vol.12
, Issue.1
, pp. 21-27
-
-
Lichtarge, O.1
Sowa, M.E.2
-
25
-
-
0035896024
-
ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
-
Armon A, Graur D, Ben-Tal N. 2001. ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 307(1):447-463.
-
(2001)
J Mol Biol
, vol.307
, Issue.1
, pp. 447-463
-
-
Armon, A.1
Graur, D.2
Ben-Tal, N.3
-
26
-
-
2542445427
-
ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
-
Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N. 2003. ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19(1):163-164.
-
(2003)
Bioinformatics
, vol.19
, Issue.1
, pp. 163-164
-
-
Glaser, F.1
Pupko, T.2
Paz, I.3
Bell, R.E.4
Bechor-Shental, D.5
Martz, E.6
Ben-Tal, N.7
-
27
-
-
0002218484
-
Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
-
Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N. 2002. Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues Bioinformatics 18(Suppl 1):71-77.
-
(2002)
Bioinformatics
, vol.18
, pp. 71-77
-
-
Pupko, T.1
Bell, R.E.2
Mayrose, I.3
Glaser, F.4
Ben-Tal, N.5
-
28
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy P, Russell RB. 2002. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 99(9):5896-5901.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, Issue.9
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
29
-
-
0042010066
-
Asymmetric mutation rates at enzyme-inhibitor interfaces: Implications for the protein-protein docking problem
-
Bradford JR, Westhead DR. 2003. Asymmetric mutation rates at enzyme-inhibitor interfaces: Implications for the protein-protein docking problem. Protein Sci 12(9):2099-2103.
-
(2003)
Protein Sci
, vol.12
, Issue.9
, pp. 2099-2103
-
-
Bradford, J.R.1
Westhead, D.R.2
-
30
-
-
0346733329
-
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
-
Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. 2004. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 13(1):190-202.
-
(2004)
Protein Sci
, vol.13
, Issue.1
, pp. 190-202
-
-
Caffrey, D.R.1
Somaroo, S.2
Hughes, J.D.3
Mintseris, J.4
Huang, E.S.5
-
31
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris J, Weng Z. 2005. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 102(31):10930-10935.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.31
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
32
-
-
1042275583
-
A dissection of specific and nonspecific protein-protein interfaces
-
Bahadur RP, Chakrabarti P, Rodier F, Janin J. 2004. A dissection of specific and nonspecific protein-protein interfaces. J Mol Biol 336(4):943-955.
-
(2004)
J Mol Biol
, vol.336
, Issue.4
, pp. 943-955
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
Janin, J.4
-
33
-
-
0031565729
-
Analysis of protein-protein interaction sites using surface patches
-
Jones S, Thornton JM. 1997. Analysis of protein-protein interaction sites using surface patches. J Mol Biol 272(1):121-132.
-
(1997)
J Mol Biol
, vol.272
, Issue.1
, pp. 121-132
-
-
Jones, S.1
Thornton, J.M.2
-
34
-
-
0032522670
-
Morphology of protein-protein interfaces
-
Larsen TA, Olson AJ, Goodsell DS. 1998. Morphology of protein-protein interfaces. Structure 6(4):421-427.
-
(1998)
Structure
, vol.6
, Issue.4
, pp. 421-427
-
-
Larsen, T.A.1
Olson, A.J.2
Goodsell, D.S.3
-
35
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Conte LL, Chothia C, Janin J. 1999. The atomic structure of protein-protein recognition sites. J Mol Biol 285(5):2177-2198.
-
(1999)
J Mol Biol
, vol.285
, Issue.5
, pp. 2177-2198
-
-
Conte, L.L.1
Chothia, C.2
Janin, J.3
-
36
-
-
0030580057
-
Antibody-antigen interactions: Contact analysis and binding site topography
-
MacCallum RM, Martin AC, Thornton JM. 1996. Antibody-antigen interactions: Contact analysis and binding site topography. J Mol Biol 262(5):732-745.
-
(1996)
J Mol Biol
, vol.262
, Issue.5
, pp. 732-745
-
-
Maccallum, R.M.1
Martin, A.C.2
Thornton, J.M.3
-
37
-
-
0037474541
-
Structural characterisation and functional significance of transient protein-protein interactions
-
Nooren IM, Thornton JM. 2003. Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol 325(5):991-1018.
-
(2003)
J Mol Biol
, vol.325
, Issue.5
, pp. 991-1018
-
-
Nooren, I.M.1
Thornton, J.M.2
-
38
-
-
0037229456
-
Rost B. Analysing six types of protein-protein interfaces
-
Ofran Y, Rost B. Analysing six types of protein-protein interfaces. 2003. J Mol Biol 325(2):377-387.
-
(2003)
J Mol Biol
, vol.325
, Issue.2
, pp. 377-387
-
-
Ofran, Y.1
-
39
-
-
19544372768
-
Hydration of protein-protein interfaces
-
Rodier F, Bahadur RP, Chakrabarti P, Janin J. 2005. Hydration of protein-protein interfaces. Proteins 60(1):36-45.
-
(2005)
Proteins
, vol.60
, Issue.1
, pp. 36-45
-
-
Rodier, F.1
Bahadur, R.P.2
Chakrabarti, P.3
Janin, J.4
-
40
-
-
1842405464
-
Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
-
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. 1997. Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect. Protein Sci 16(1):53-64.
-
(1997)
Protein Sci
, vol.16
, Issue.1
, pp. 53-64
-
-
Tsai, C.J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
41
-
-
0028332007
-
A role for surface hydrophobicity in protein-protein recognition
-
Young L, Jernigan RL, Covell DG. 1994. A role for surface hydrophobicity in protein-protein recognition. Protein Sci 3(5):717-729.
-
(1994)
Protein Sci
, vol.3
, Issue.5
, pp. 717-729
-
-
Young, L.1
Jernigan, R.L.2
Covell, D.G.3
-
42
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones S, Thornton JM. 1996. Principles of protein-protein interactions. Proc Natl Acad Sci USA 93(1):13-20.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, Issue.1
, pp. 13-20
-
-
Jones, S.1
Thornton, J.M.2
-
43
-
-
0041312697
-
Diversity of protein-protein interactions
-
Nooren IM, Thornton JM. 2003. Diversity of protein-protein interactions. EMBO J 22(14):3486-3492.
-
(2003)
EMBO J
, vol.22
, Issue.14
, pp. 3486-3492
-
-
Nooren, I.M.1
Thornton, J.M.2
-
44
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan AA, Thorn KS. 1998. Anatomy of hot spots in protein interfaces. J Mol Biol 280(1):1-9.
-
(1998)
J Mol Biol
, vol.280
, Issue.1
, pp. 1-9
-
-
Bogan, A.A.1
Thorn, K.S.2
-
45
-
-
0028916599
-
A hot spot of binding energy in a hormone-receptor interface
-
Clackson T, Wells JA. 1995. A hot spot of binding energy in a hormone-receptor interface. Science 267(5196):383-386.
-
(1995)
Science
, vol.267
, Issue.5196
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
47
-
-
0036468396
-
Protein-protein association kinetics and protein docking
-
Camacho CJ, Vajda S. 2002. Protein-protein association kinetics and protein docking. Curr Opin Struct Biol 12(1):36-40.
-
(2002)
Curr Opin Struct Biol
, vol.12
, Issue.1
, pp. 36-40
-
-
Camacho, C.J.1
Vajda, S.2
-
48
-
-
0036306236
-
On the role of electrostatic interactions in the design of protein-protein interfaces
-
Sheinerman FB, Honig B. 2002. On the role of electrostatic interactions in the design of protein-protein interfaces. J Mol Biol 318(1):161-177.
-
(2002)
J Mol Biol
, vol.318
, Issue.1
, pp. 161-177
-
-
Sheinerman, F.B.1
Honig, B.2
-
49
-
-
0031565725
-
Prediction of protein-protein interaction sites using patch analysis
-
Jones S, Thornton JM. 1997. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 272(1):133-143.
-
(1997)
J Mol Biol
, vol.272
, Issue.1
, pp. 133-143
-
-
Jones, S.1
Thornton, J.M.2
-
50
-
-
0030997363
-
Hydrophobic patches on protein subunit interfaces: Characteristics and prediction
-
Lijnzaad P, Argos P. 1997. Hydrophobic patches on protein subunit interfaces: Characteristics and prediction. Proteins 28(3):333-343.
-
(1997)
Proteins
, vol.28
, Issue.3
, pp. 333-343
-
-
Lijnzaad, P.1
Argos, P.2
-
51
-
-
1542390499
-
Identification of protein-protein interaction sites from docking energy landscapes
-
Fernández-Recio J, Totrov M, Abagyan R. 2004. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 335(3):843-865.
-
(2004)
J Mol Biol
, vol.335
, Issue.3
, pp. 843-865
-
-
Fernández-Recio, J.1
Totrov, M.2
Abagyan, R.3
-
52
-
-
33947360625
-
PIER: Protein interface recognition for structural proteomics
-
Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R. 2007. PIER: Protein interface recognition for structural proteomics. Proteins 67(2):400-417.
-
(2007)
Proteins
, vol.67
, Issue.2
, pp. 400-417
-
-
Kufareva, I.1
Budagyan, L.2
Raush, E.3
Totrov, M.4
Abagyan, R.5
-
53
-
-
11144325691
-
Partial least squares regression: A tutorial
-
Geladi P, Kowalski B. 1986. Partial least squares regression: A tutorial. Analytica Chimica Acta 185:1-17.
-
(1986)
Analytica Chimica Acta
, vol.185
, pp. 1-17
-
-
Geladi, P.1
Kowalski, B.2
-
54
-
-
84872115717
-
Pleckstrin homology (PH) domains and phosphoinositides
-
Lemmon MA. 2007. Pleckstrin homology (PH) domains and phosphoinositides. Biochem Soc Symp 74:81-93.
-
(2007)
Biochem Soc Symp
, vol.74
, pp. 81-93
-
-
Lemmon, M.A.1
-
55
-
-
38549092474
-
Membrane recognition by phospholipid-binding domains
-
Lemmon MA. 2008. Membrane recognition by phospholipid-binding domains. Nat Rev Mol Cell Biol 9(2):99-111.
-
(2008)
Nat Rev Mol Cell Biol
, vol.9
, Issue.2
, pp. 99-111
-
-
Lemmon, M.A.1
-
56
-
-
85055508211
-
Computational identification of novel peripheral protein-membrane interactions
-
Kufareva I, Dancea F, Kiran MR, Polonskaya Z, Overduin M, Abagyan R. 2008. Computational identification of novel peripheral protein-membrane interactions. FASEB J 22:811-815.
-
(2008)
FASEB J
, vol.22
, pp. 811-815
-
-
Kufareva, I.1
Dancea, F.2
Kiran, M.R.3
Polonskaya, Z.4
Overduin, M.5
Abagyan, R.6
-
57
-
-
41949126415
-
In silico-in vitro screening of protein-protein interactions: Towards the next generation of therapeutics
-
Villoutreix BO, Bastard K, Sperandio O, Fahraeus R, Poyet J-L, Calvo F, Deprez B, Miteva MA. 2008. In silico-in vitro screening of protein-protein interactions: Towards the next generation of therapeutics. Curr Pharm Biotechnol 9(2):103-122.
-
(2008)
Curr Pharm Biotechnol
, vol.9
, Issue.2
, pp. 103-122
-
-
Villoutreix, B.O.1
Bastard, K.2
Sperandio, O.3
Fahraeus, R.4
Poyet, J.-L.5
Calvo, F.6
Deprez, B.7
Miteva, M.A.8
-
58
-
-
1842861590
-
Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications
-
Wodak SJ, Méndez R. 2004. Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 14(2):242-249.
-
(2004)
Curr Opin Struct Biol
, vol.14
, Issue.2
, pp. 242-249
-
-
Wodak, S.J.1
Méndez, R.2
-
59
-
-
41949099167
-
Recognition-induced conformational changes in protein-protein docking
-
Lensink MF, Mendez R. 2008. Recognition-induced conformational changes in protein-protein docking. Curr Pharm Biotechnol 9(2):77-86.
-
(2008)
Curr Pharm Biotechnol
, vol.9
, Issue.2
, pp. 77-86
-
-
Lensink, M.F.1
Mendez, R.2
-
60
-
-
33745298429
-
Rational design of inhibitors that bind to inactive kinase conformations
-
Liu Y, Gray NS. 2006. Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol 2(7):358-364.
-
(2006)
Nat Chem Biol
, vol.2
, Issue.7
, pp. 358-364
-
-
Liu, Y.1
Gray, N.S.2
-
61
-
-
0042357240
-
Structure of a c-kit product complex reveals the basis for kinase transactivation
-
Mol CD, Lim KB, Sridhar V, Zou H, Chien EYT, Sang B-C, Nowakowski J, Kassel DB, Cronin CN, McRee DE. 2003. Structure of a c-kit product complex reveals the basis for kinase transactivation. J Biol Chem 278(34):31461-31464.
-
(2003)
J Biol Chem
, vol.278
, Issue.34
, pp. 31461-31464
-
-
Mol, C.D.1
Lim, K.B.2
Sridhar, V.3
Zou, H.4
Chien, E.5
Sang, B.-C.6
Nowakowski, J.7
Kassel, D.B.8
Cronin, C.N.9
McRee, D.E.10
-
62
-
-
0035037143
-
A proposed structural model for amyloid fibril elongation: Domain swapping forms an interdigitating beta-structure polymer
-
Sinha N, Tsai CJ, Nussinov R. 2001. A proposed structural model for amyloid fibril elongation: Domain swapping forms an interdigitating beta-structure polymer. Protein Eng 14(2):93-103.
-
(2001)
Protein Eng
, vol.14
, Issue.2
, pp. 93-103
-
-
Sinha, N.1
Tsai, C.J.2
Nussinov, R.3
-
63
-
-
41949131198
-
Sequence and structural determinants of strand swapping in cadherin domains: Do all cadherins bind through the same adhesive interface?
-
Posy S, Shapiro L, Honig B. 2008. Sequence and structural determinants of strand swapping in cadherin domains: Do all cadherins bind through the same adhesive interface? J Mol Biol 378(4):952-966.
-
(2008)
J Mol Biol
, vol.378
, Issue.4
, pp. 952-966
-
-
Posy, S.1
Shapiro, L.2
Honig, B.3
-
64
-
-
41949111630
-
Recent progress and future directions in protein-protein docking
-
Ritchie DW. 2008. Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 9(1):1-15.
-
(2008)
Curr Protein Pept Sci
, vol.9
, Issue.1
, pp. 1-15
-
-
Ritchie, D.W.1
-
65
-
-
21644447570
-
Improving CAPRI predictions: Optimized desolvation for rigid-body docking
-
Fernandez-Recio J, Abagyan R, Totrov M. 2005. Improving CAPRI predictions: Optimized desolvation for rigid-body docking. Proteins 60(2):308-313.
-
(2005)
Proteins
, vol.60
, Issue.2
, pp. 308-313
-
-
Fernandez-Recio, J.1
Abagyan, R.2
Totrov, M.3
-
66
-
-
0028410583
-
Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy
-
Totrov M, Abagyan R. 1994. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nat Struct Biol 1(4):259-263.
-
(1994)
Nat Struct Biol
, vol.1
, Issue.4
, pp. 259-263
-
-
Totrov, M.1
Abagyan, R.2
-
67
-
-
0027955787
-
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
-
Abagyan R, Totrov M. 1994. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 235(3):983-1002.
-
(1994)
J Mol Biol
, vol.235
, Issue.3
, pp. 983-1002
-
-
Abagyan, R.1
Totrov, M.2
-
68
-
-
50549092426
-
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions
-
Ritchie DW, Kozakov D, Vajda S. 2008. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics 24(17):1865-1873.
-
(2008)
Bioinformatics
, vol.24
, Issue.17
, pp. 1865-1873
-
-
Ritchie, D.W.1
Kozakov, D.2
Vajda, S.3
-
69
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin I, Ma B, Wolfson H, Nussinov R. 2002. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47(4):409-443.
-
(2002)
Proteins
, vol.47
, Issue.4
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
70
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith GR, Sternberg MJ. 2002. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 12(1):28-35.
-
(2002)
Curr Opin Struct Biol
, vol.12
, Issue.1
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.2
-
71
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: Current status of docking methods
-
Méndez R, Leplae R, Maria LD, Wodak SJ. 2003. Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins 52(1):51-67.
-
(2003)
Proteins
, vol.52
, Issue.1
, pp. 51-67
-
-
Méndez, R.1
Leplae, R.2
Maria, L.D.3
Wodak, S.J.4
-
72
-
-
21644469377
-
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
-
Méndez R, Leplae R, Lensink MF, Wodak SJ. 2005. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60(2):150-169.
-
(2005)
Proteins
, vol.60
, Issue.2
, pp. 150-169
-
-
Méndez, R.1
Leplae, R.2
Lensink, M.F.3
Wodak, S.J.4
-
73
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
-
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. 2003. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331(1):281-299.
-
(2003)
J Mol Biol
, vol.331
, Issue.1
, pp. 281-299
-
-
Gray, J.J.1
Moughon, S.2
Wang, C.3
Schueler-Furman, O.4
Kuhlman, B.5
Rohl, C.A.6
Baker, D.7
-
74
-
-
36749045652
-
Protein-protein docking: Progress in CAPRI rounds 6-12 using a combination of methods: The introduction of steered solvated molecular dynamics
-
Heifetz A, Pal S, Smith GR. 2007. Protein-protein docking: Progress in CAPRI rounds 6-12 using a combination of methods: The introduction of steered solvated molecular dynamics. Proteins 69(4):816-822.
-
(2007)
Proteins
, vol.69
, Issue.4
, pp. 816-822
-
-
Heifetz, A.1
Pal, S.2
Smith, G.R.3
-
75
-
-
36749082073
-
A holistic approach to protein docking
-
Qin S, Zhou H-X. 2007. A holistic approach to protein docking. Proteins 69(4):743-749.
-
(2007)
Proteins
, vol.69
, Issue.4
, pp. 743-749
-
-
Qin, S.1
Zhou, H.-X.2
-
76
-
-
44349160733
-
Protein-protein docking by simulating the process of association subject to biochemical constraints
-
Motiejunas D, Gabdoulline R, Wang T, Feldman-Salit A, Johann T, Winn PJ, Wade RC. 2008. Protein-protein docking by simulating the process of association subject to biochemical constraints. Proteins 71(4):1955-1969.
-
(2008)
Proteins
, vol.71
, Issue.4
, pp. 1955-1969
-
-
Motiejunas, D.1
Gabdoulline, R.2
Wang, T.3
Feldman-Salit, A.4
Johann, T.5
Winn, P.J.6
Wade, R.C.7
-
77
-
-
0036510961
-
Identification and mapping of small-molecule binding sites in proteins: Computational tools for structure-based drug design
-
Sotriffer C, Klebe G. 2002. Identification and mapping of small-molecule binding sites in proteins: Computational tools for structure-based drug design. Farmaco 57(3):243-251.
-
(2002)
Farmaco
, vol.57
, Issue.3
, pp. 243-251
-
-
Sotriffer, C.1
Klebe, G.2
-
78
-
-
34548289911
-
Free resources to assist structure-based virtual ligand screening experiments
-
Villoutreix BO, Renault N, Lagorce D, Sperandio O, Montes M, Miteva MA. 2007. Free resources to assist structure-based virtual ligand screening experiments. Curr Protein Pept Sci 8(4):381-411.
-
(2007)
Curr Protein Pept Sci
, vol.8
, Issue.4
, pp. 381-411
-
-
Villoutreix, B.O.1
Renault, N.2
Lagorce, D.3
Sperandio, O.4
Montes, M.5
Miteva, M.A.6
-
79
-
-
21044444449
-
Pocketome via comprehensive identification and classification of ligand binding envelopes
-
An J, Totrov M, Abagyan R. 2005. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics 4(6):752-761.
-
(2005)
Mol Cell Proteomics
, vol.4
, Issue.6
, pp. 752-761
-
-
An, J.1
Totrov, M.2
Abagyan, R.3
-
80
-
-
47249102090
-
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
-
Bottegoni G, Kufareva I, Totrov M, Abagyan R. 2008. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des 22(5):311-325.
-
(2008)
J Comput Aided Mol Des
, vol.22
, Issue.5
, pp. 311-325
-
-
Bottegoni, G.1
Kufareva, I.2
Totrov, M.3
Abagyan, R.4
-
81
-
-
41349095752
-
New method for the assessment of all drug-like pockets across a structural genome
-
Nicola G, Smith CA, Abagyan R. 2008. New method for the assessment of all drug-like pockets across a structural genome. J Comput Biol 15(3):231-240.
-
(2008)
J Comput Biol
, vol.15
, Issue.3
, pp. 231-240
-
-
Nicola, G.1
Smith, C.A.2
Abagyan, R.3
-
82
-
-
33749506205
-
Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening
-
Laurie ATR, Jackson RM. 2006. Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sci 7(5):395-406.
-
(2006)
Curr Protein Pept Sci
, vol.7
, Issue.5
, pp. 395-406
-
-
Laurie, A.1
Jackson, R.M.2
-
83
-
-
0031302358
-
Flexible protein-ligand docking by global energy optimization in internal coordinates
-
Totrov M, Abagyan R. 1997. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 29(Suppl 1):215-220.
-
(1997)
Proteins
, vol.29
, pp. 215-220
-
-
Totrov, M.1
Abagyan, R.2
-
84
-
-
41949132916
-
Flexible ligand docking to multiple receptor conformations: A practical alternative
-
Totrov M, Abagyan R. 2008. Flexible ligand docking to multiple receptor conformations: A practical alternative. Curr Opin Struct Biol 18(2):178-184.
-
(2008)
Curr Opin Struct Biol
, vol.18
, Issue.2
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
85
-
-
0027185404
-
A method to configure protein side-chains from the main-chain trace in homology modelling
-
Eisenmenger F, Argos P, Abagyan R. 1993. A method to configure protein side-chains from the main-chain trace in homology modelling. J Mol Biol 231(3):849-860.
-
(1993)
J Mol Biol
, vol.231
, Issue.3
, pp. 849-860
-
-
Eisenmenger, F.1
Argos, P.2
Abagyan, R.3
-
86
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. 2006. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 49(2):534-553.
-
(2006)
J Med Chem
, vol.49
, Issue.2
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
-
87
-
-
0033137131
-
Prediction of the binding energy for small molecules, peptides and proteins
-
Schapira M, Totrov M, Abagyan R. 1999. Prediction of the binding energy for small molecules, peptides and proteins. J Mol Recog 12(3):177-190.
-
(1999)
J Mol Recog
, vol.12
, Issue.3
, pp. 177-190
-
-
Schapira, M.1
Totrov, M.2
Abagyan, R.3
-
88
-
-
60549086155
-
Four-dimensional docking: A fast and accurate account of discrete receptor flexibility in ligand docking
-
Bottegoni G, Kufareva I, Totrov M, Abagyan R. 2009. Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. Journal of Medicinal Chemistry 52(2):397-406.
-
(2009)
Journal of Medicinal Chemistry
, vol.52
, Issue.2
, pp. 397-406
-
-
Bottegoni, G.1
Kufareva, I.2
Totrov, M.3
Abagyan, R.4
-
89
-
-
58149102648
-
Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states
-
Kufareva I, Abagyan R. 2008. Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. Journal of Medicinal Chemistry 51(24):7921-7932.
-
(2008)
Journal of Medicinal Chemistry
, vol.51
, Issue.24
, pp. 7921-7932
-
-
Kufareva, I.1
Abagyan, R.2
|