-
1
-
-
0037452709
-
Binding of small molecules to an adaptive protein-protein interface
-
Arkin, M.R., Randal, M., DeLano, W.L., Hyde, J., Luong, T.N., Oslob, J.D., Raphael, D.R., Taylor, L., Wang, J., McDowell, R.S., et al. 2003. Binding of small molecules to an adaptive protein-protein interface. Proc. Natl. Acad. Sci. 100: 1603-1608.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 1603-1608
-
-
Arkin, M.R.1
Randal, M.2
DeLano, W.L.3
Hyde, J.4
Luong, T.N.5
Oslob, J.D.6
Raphael, D.R.7
Taylor, L.8
Wang, J.9
McDowell, R.S.10
-
2
-
-
0027238108
-
A computer vision based technique for 3-D sequence-independent structural comparison of proteins
-
Bachar, O., Fischer, D., Nussinov, R., and Wolfson, H. 1993. A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Eng. 6: 279-288.
-
(1993)
Protein Eng.
, vol.6
, pp. 279-288
-
-
Bachar, O.1
Fischer, D.2
Nussinov, R.3
Wolfson, H.4
-
3
-
-
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
-
4
-
-
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
-
5
-
-
0036721253
-
Stability of macromolecular complexes
-
Brooijmans, N., Sharp, K.A., and Kuntz, I.D. 2002. Stability of macromolecular complexes. Proteins 48: 645-653.
-
(2002)
Proteins
, vol.48
, pp. 645-653
-
-
Brooijmans, N.1
Sharp, K.A.2
Kuntz, I.D.3
-
6
-
-
0037093645
-
Dissecting protein-protein recognition sites
-
Chakrabarti, P. and Janin, J. 2002. Dissecting protein-protein recognition sites. Proteins 47: 334-343.
-
(2002)
Proteins
, vol.47
, pp. 334-343
-
-
Chakrabarti, P.1
Janin, J.2
-
7
-
-
0027122748
-
Proteins. One thousand families for the molecular biologist
-
Chothia, C. 1992. Proteins. One thousand families for the molecular biologist. Nature 357: 543-544.
-
(1992)
Nature
, vol.357
, pp. 543-544
-
-
Chothia, C.1
-
8
-
-
0016708122
-
Principles of protein-protein recognition
-
Chothia, C. and Janin, J. 1975. Principles of protein-protein recognition. Nature 256: 705-708.
-
(1975)
Nature
, vol.256
, pp. 705-708
-
-
Chothia, C.1
Janin, J.2
-
9
-
-
0026335990
-
Rational design of receptor-specific variants of human growth hormone
-
Cunningham, B.C. and Wells, J.A. 1991. Rational design of receptor-specific variants of human growth hormone. Proc. Natl. Acad. Sci. 88: 3407-3411.
-
(1991)
Proc. Natl. Acad. Sci.
, vol.88
, pp. 3407-3411
-
-
Cunningham, B.C.1
Wells, J.A.2
-
10
-
-
0036469060
-
Unraveling hot spots in binding interfaces: Progress and challenges
-
DeLano, W.L. 2002. Unraveling hot spots in binding interfaces: Progress and challenges. Curr. Opin. Struct. Biol. 12: 14-20.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 14-20
-
-
DeLano, W.L.1
-
11
-
-
0034681465
-
Convergent solution to binding at a protein-protein interface
-
DeLano, W.L., Ultsch, M.H., deVos, A.M., and Wells, J.A. 2000. Convergent solution to binding at a protein-protein interface. Science 287: 1279-1283.
-
(2000)
Science
, vol.287
, pp. 1279-1283
-
-
DeLano, W.L.1
Ultsch, M.H.2
DeVos, A.M.3
Wells, J.A.4
-
12
-
-
0036122073
-
Prediction of protein-protein sites in heterocomplexes with neural networks
-
Fariselli, P., Pazos, F., Valencia, A., and Casadio, R. 2002, Prediction of protein-protein sites in heterocomplexes with neural networks. Eur. J. Biochem. 269: 1356-1361.
-
(2002)
Eur. J. Biochem.
, vol.269
, pp. 1356-1361
-
-
Fariselli, P.1
Pazos, F.2
Valencia, A.3
Casadio, R.4
-
13
-
-
0037422589
-
Insufficiently dehydrated hydrogen bonds as determinants of protein interactions
-
Fernández, A. and Scheraga, H.A. 2003. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc. Natl. Acad. Sci. 100: 113-118.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 113-118
-
-
Fernández, A.1
Scheraga, H.A.2
-
14
-
-
0028230909
-
Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: Potential implications to evolution and to protein folding
-
Fischer, D., Wolfson, H., Lin, S.L., and Nussinov, R. 1994. Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: Potential implications to evolution and to protein folding. Protein Sci. 3: 769-778.
-
(1994)
Protein Sci.
, vol.3
, pp. 769-778
-
-
Fischer, D.1
Wolfson, H.2
Lin, S.L.3
Nussinov, R.4
-
16
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S. and Henikoff, J. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. 89: 10915-10919.
-
(1992)
Proc. Natl. Acad. Sci.
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.2
-
17
-
-
0034213559
-
Conservation of polar residues as hot spots at protein interfaces
-
Hu, Z., Ma, B., Wolfson, H., and Nussinov, R. 2000. Conservation of polar residues as hot spots at protein interfaces. Proteins 39: 331-342.
-
(2000)
Proteins
, vol.39
, pp. 331-342
-
-
Hu, Z.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
18
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones, S. and Thornton, J.M. 1996. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. 93: 13-20.
-
(1996)
Proc. Natl. Acad. Sci.
, vol.93
, pp. 13-20
-
-
Jones, S.1
Thornton, J.M.2
-
19
-
-
0031565729
-
Analysis of protein-protein interaction sites using surface patches
-
-. 1997. Analysis of protein-protein interaction sites using surface patches. J. Mol. Biol. 272: 121-132.
-
(1997)
J. Mol. Biol.
, vol.272
, pp. 121-132
-
-
-
20
-
-
0026572775
-
Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
-
Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., and Vakser, I.A. 1992. Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. 89: 2195-2199.
-
(1992)
Proc. Natl. Acad. Sci.
, vol.89
, pp. 2195-2199
-
-
Katchalski-Katzir, E.1
Shariv, I.2
Eisenstein, M.3
Friesem, A.A.4
Aflalo, C.5
Vakser, I.A.6
-
21
-
-
0031678069
-
Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions
-
Keskin, O., Bahar, I., Badretdinov, A.Y., Ptitsyn, O.B., and Jernigan, R.L. 1998. Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Sci. 7: 2578-2586.
-
(1998)
Protein Sci.
, vol.7
, pp. 2578-2586
-
-
Keskin, O.1
Bahar, I.2
Badretdinov, A.Y.3
Ptitsyn, O.B.4
Jernigan, R.L.5
-
22
-
-
0004072904
-
Protein-protein recognition
-
(ed. C. Kleanthous). Oxford University Press, New York
-
Kleanthous, C. 2000. Protein-protein recognition. In Frontiers in molecular biology (ed. C. Kleanthous). Oxford University Press, New York.
-
(2000)
Frontiers in Molecular Biology
-
-
Kleanthous, C.1
-
23
-
-
0034283147
-
Specificity in protein-protein interactions: The structural basis for dual recognition in endonuclease colicin-immunity protein complexes
-
Kuhlmann, U.C., Pommer, A.J., Moore, G.R., James, R., and Kleanthous, C. 2000. Specificity in protein-protein interactions: The structural basis for dual recognition in endonuclease colicin-immunity protein complexes. J. Mol. Biol. 301: 1163-1178.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 1163-1178
-
-
Kuhlmann, U.C.1
Pommer, A.J.2
Moore, G.R.3
James, R.4
Kleanthous, C.5
-
24
-
-
0007946299
-
Fluctuations in ion pairs and their stabilities in proteins
-
Kumar, S. and Nussinov, R. 2001. Fluctuations in ion pairs and their stabilities in proteins. Proteins 41: 485-497.
-
(2001)
Proteins
, vol.41
, pp. 485-497
-
-
Kumar, S.1
Nussinov, R.2
-
25
-
-
0033621044
-
The maximal affinity of ligands
-
Kuntz, I.D., Chen, K., Sharp, K.A., and Kollman, P.A. 1999. The maximal affinity of ligands. Proc. Natl. Acad. Sci. 96: 9997-10002.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 9997-10002
-
-
Kuntz, I.D.1
Chen, K.2
Sharp, K.A.3
Kollman, P.A.4
-
26
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge, O., Bourne, H.R., and Cohen, F.E. 1996. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257: 342-358.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
27
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
LoConte, L., Chothia, C., and Janin, J. 1999. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285: 2177-2198.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 2177-2198
-
-
LoConte, L.1
Chothia, C.2
Janin, J.3
-
28
-
-
0035366379
-
Protein functional epitopes: Hot spots, dynamics and combinatorial libraries
-
Ma, B., Wolfson, H.J., and Nussinov, R. 2001. Protein functional epitopes: Hot spots, dynamics and combinatorial libraries. Curr. Opin. Struct. Biol. 11: 364-369.
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 364-369
-
-
Ma, B.1
Wolfson, H.J.2
Nussinov, R.3
-
29
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
-
Ma, B., Shatsky, M., Wolfson, H.J., and Nussinov, R. 2002. Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations. Protein Sci. 11: 184-197.
-
(2002)
Protein Sci.
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.J.3
Nussinov, R.4
-
30
-
-
0037609791
-
Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
-
Ma, B., Elkayam, T., Wolfson, H., and Nussinov, R, 2003. Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl. Acad. Sci. 100: 5772-5777.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 5772-5777
-
-
Ma, B.1
Elkayam, T.2
Wolfson, H.3
Nussinov, R.4
-
31
-
-
0032527783
-
Protein folds and functions
-
Martin, A.C.R., Orengo, C.A., Hutchinson, E.G., Jones, S., Karmirantzou, M., Laskowski, R.A., Mitchell, J.B.O., Taroni, C., and Thornton, J.M. 1998. Protein folds and functions. Structure 6: 875-884.
-
(1998)
Structure
, vol.6
, pp. 875-884
-
-
Martin, A.C.R.1
Orengo, C.A.2
Hutchinson, E.G.3
Jones, S.4
Karmirantzou, M.5
Laskowski, R.A.6
Mitchell, J.B.O.7
Taroni, C.8
Thornton, J.M.9
-
32
-
-
0023645203
-
Interior and surface of monomeric proteins
-
Miller, S., Janin, J., Lesk, A.M., and Chothia, C. 1987. Interior and surface of monomeric proteins. J. Mol. Biol. 196: 641-656.
-
(1987)
J. Mol. Biol.
, vol.196
, pp. 641-656
-
-
Miller, S.1
Janin, J.2
Lesk, A.M.3
Chothia, C.4
-
34
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
35
-
-
0036384350
-
One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
-
Nagano, N., Orengo, C.A., and Thornton, J.M. 2002. One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321: 741-765.
-
(2002)
J. Mol. Biol.
, vol.321
, pp. 741-765
-
-
Nagano, N.1
Orengo, C.A.2
Thornton, J.M.3
-
36
-
-
0037474541
-
Structural characterisation and functional significance of transient protein-protein interactions
-
Nooren, I.M.A. and Thornton, J.M. 2003. Structural characterisation and functional significance of transient protein-protein interactions. J. Mol. Biol. 325: 991-1018.
-
(2003)
J. Mol. Biol.
, vol.325
, pp. 991-1018
-
-
Nooren, I.M.A.1
Thornton, J.M.2
-
37
-
-
0025719208
-
Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques
-
Nussinov, R. and Wolfson, H.J. 1991. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc. Natl. Acad. Sci. 88: 10495-10499.
-
(1991)
Proc. Natl. Acad. Sci.
, vol.88
, pp. 10495-10499
-
-
Nussinov, R.1
Wolfson, H.J.2
-
38
-
-
0033150686
-
From protein structure to function
-
Orengo, C.A., Todd, A.E., and Thornton, J.M. 1999. From protein structure to function. Curr. Opin. Struct. Biol. 9: 374-382.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 374-382
-
-
Orengo, C.A.1
Todd, A.E.2
Thornton, J.M.3
-
39
-
-
84956971981
-
Multiprot: A multiple protein structural alignment
-
Shatsky, M., Nussinov, R., and Wolfson, H, 2002. Multiprot: A multiple protein structural alignment. In Proceedings of ALGO 02. Algorithms in Bioinformatics. Lecture Notes in Computer Science, Vol. 2452, pp. 235-250.
-
(2002)
Proceedings of ALGO 02. Algorithms in Bioinformatics. Lecture Notes in Computer Science
, vol.2452
, pp. 235-250
-
-
Shatsky, M.1
Nussinov, R.2
Wolfson, H.3
-
40
-
-
1842559884
-
A method for simultaneous alignment of multiple protein structures
-
in press
-
-. 2003. A method for simultaneous alignment of multiple protein structures. Proteins (in press).
-
(2003)
Proteins
-
-
-
41
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressivemultiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressivemultiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
42
-
-
0033757840
-
From structure to function: Approaches and limitations
-
Thornton, J.M., Todd, A.E., Milburn, D., Borkakoti, N., and Orengo, C.A. 2000. From structure to function: Approaches and limitations. Nat. Struct. Biol. 7: 991-994.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 991-994
-
-
Thornton, J.M.1
Todd, A.E.2
Milburn, D.3
Borkakoti, N.4
Orengo, C.A.5
-
43
-
-
0036776124
-
Sequence and structural differences between enzyme and nonenzyme homologs
-
Todd, A.E., Orengo, C.A., and Thornton, J.M. 2002. Sequence and structural differences between enzyme and nonenzyme homologs. Structure 10: 1435-1451.
-
(2002)
Structure
, vol.10
, pp. 1435-1451
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
44
-
-
0023818432
-
A transportable interactive package for the statistical analysis and handling of sequence data
-
Tramontano, A. and Macchiato, M.F. 1994. A transportable interactive package for the statistical analysis and handling of sequence data. Comput. Biol. Med. 18: 113-122.
-
(1994)
Comput. Biol. Med.
, vol.18
, pp. 113-122
-
-
Tramontano, A.1
Macchiato, M.F.2
-
45
-
-
0030756203
-
Hydrophobic folding units at protein-protein interfaces: Implication to protein folding and to protein-protein association
-
Tsai, C.J. and Nussinov, R. 1997. Hydrophobic folding units at protein-protein interfaces: Implication to protein folding and to protein-protein association. Protein Sci. 6: 1426-1437.
-
(1997)
Protein Sci.
, vol.6
, pp. 1426-1437
-
-
Tsai, C.J.1
Nussinov, R.2
-
46
-
-
0030602896
-
A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
-
Tsai, C.J., Lin, S.L., Wolfson, H.J., and Nussinov, R. 1996. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J. Mol. Biol. 260: 604-620.
-
(1996)
J. Mol. Biol.
, vol.260
, pp. 604-620
-
-
Tsai, C.J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
47
-
-
1842405464
-
Studies of protein-protein interfaces: Statistical analysis of the hydrophobic effect
-
-. 1997. Studies of protein-protein interfaces: Statistical analysis of the hydrophobic effect. Protein Sci. 6: 53-64.
-
(1997)
Protein Sci
, vol.6
, pp. 53-64
-
-
-
48
-
-
0030768266
-
Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes
-
Tsai, C.J., Xu, D., and Nussinov, R. 1998a. Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes. Protein Sci. 6: 1793-1805.
-
(1998)
Protein Sci.
, vol.6
, pp. 1793-1805
-
-
Tsai, C.J.1
Xu, D.2
Nussinov, R.3
-
49
-
-
0031868211
-
Protein folding via binding and vice versa
-
-. 1998b. Protein folding via binding and vice versa. Fold. Des. 3: R71-R80.
-
(1998)
Fold. Des.
, vol.3
-
-
-
50
-
-
0035914476
-
Conservation helps to identify biologically relevant crystal contacts
-
Valdar, W.S.J. and Thornton, J.M. 2001a. Conservation helps to identify biologically relevant crystal contacts. J. Mol. Biol. 313: 339-416.
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 339-416
-
-
Valdar, W.S.J.1
Thornton, J.M.2
-
51
-
-
0035178383
-
Protein-protein interfaces: Analysis of amino acid conservation in homodimers
-
-. 2001b. Protein-protein interfaces: Analysis of amino acid conservation in homodimers. Proteins 42: 108-124.
-
(2001)
Proteins
, vol.42
, pp. 108-124
-
-
-
52
-
-
0032512424
-
Specificity in protein-protein recognition: Conserved Im9 residues are the major determinants of stability in the colicin E9 DNase-Im9 complex
-
Wallis, R., Leung, K.Y., Osborne, M.J., James, R., Moore, G.R., and Kleanthous, C. 1998. Specificity in protein-protein recognition: Conserved Im9 residues are the major determinants of stability in the colicin E9 DNase-Im9 complex. Biochemistry 37: 476-485.
-
(1998)
Biochemistry
, vol.37
, pp. 476-485
-
-
Wallis, R.1
Leung, K.Y.2
Osborne, M.J.3
James, R.4
Moore, G.R.5
Kleanthous, C.6
-
53
-
-
0029982521
-
Hematopoietic receptor complexes
-
Wells, J.A. and deVos, A.M. 1996. Hematopoietic receptor complexes. Annu. Rev. Biochem. 65: 609-634.
-
(1996)
Annu. Rev. Biochem.
, vol.65
, pp. 609-634
-
-
Wells, J.A.1
DeVos, A.M.2
-
54
-
-
0031913197
-
Mechanism and evolution of protein dimerization
-
Xu, D., Tsai, C.J., and Nussinov, R. 1998. Mechanism and evolution of protein dimerization. Protein Sci. 7: 533-544.
-
(1998)
Protein Sci.
, vol.7
, pp. 533-544
-
-
Xu, D.1
Tsai, C.J.2
Nussinov, R.3
|