-
1
-
-
0035896024
-
ConSurf: An algorithmic tool for the identification of functional regions in proteins
-
Armon A., Grauer D., Ben-Tal N. ConSurf. an algorithmic tool for the identification of functional regions in proteins J. Mol. Biol. 307:2001;447-463
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 447-463
-
-
Armon, A.1
Grauer, D.2
Ben-Tal, N.3
-
2
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2002;235-242
-
(2002)
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
-
3
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan A.A., Thorn K.S. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280:1998;1-9
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 1-9
-
-
Bogan, A.A.1
Thorn, K.S.2
-
4
-
-
0028247281
-
Side-chain entropy and packing in proteins
-
Bromberg S., Dill K.A. Side-chain entropy and packing in proteins. Protein Sci. 3:1994;997-1009
-
(1994)
Protein Sci.
, vol.3
, pp. 997-1009
-
-
Bromberg, S.1
Dill, K.A.2
-
5
-
-
0037093645
-
Dissecting protein-protein recognition sites
-
Chakrabarti P., Janin J. Dissecting protein-protein recognition sites. Proteins. 47:2002;334-343
-
(2002)
Proteins
, vol.47
, pp. 334-343
-
-
Chakrabarti, P.1
Janin, J.2
-
6
-
-
0031599142
-
Mersenne twister: A 623-deimentionally equidistributed uniform pseudo random number generator
-
Chavez R.M., Cooper G.F. Mersenne twister. a 623-deimentionally equidistributed uniform pseudo random number generator ACM Trans. Model. Comput. Simul. 8:1998;1-30
-
(1998)
ACM Trans. Model. Comput. Simul.
, vol.8
, pp. 1-30
-
-
Chavez, R.M.1
Cooper, G.F.2
-
7
-
-
0016708122
-
Principles of protein-protein recognition
-
Chothia C., Janin J. Principles of protein-protein recognition. Nature. 256:1975;705-708
-
(1975)
Nature
, vol.256
, pp. 705-708
-
-
Chothia, C.1
Janin, J.2
-
8
-
-
0028916599
-
A hot spot of binding energy in a hormone-receptor interface
-
Clackson T., Wells J.A. A hot spot of binding energy in a hormone-receptor interface. Science. 267:1995;383-386
-
(1995)
Science
, vol.267
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
9
-
-
0036469060
-
Unraveling hot spots in binding interfaces: Progress and challenges
-
DeLano W.L. Unraveling hot spots in binding interfaces. progress and challenges Curr. Opin. Struct. Biol. 12:2002;14-20
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 14-20
-
-
Delano, W.L.1
-
10
-
-
0034681465
-
Convergent solutions to binding at a protein-protein interface
-
DeLano W.L., Ultsch M.H., de Vos A.M., Wells J.A. Convergent solutions to binding at a protein-protein interface. Science. 287:2000;1279-1283
-
(2000)
Science
, vol.287
, pp. 1279-1283
-
-
Delano, W.L.1
Ultsch, M.H.2
De Vos, A.M.3
Wells, J.A.4
-
11
-
-
84956979675
-
Efficient unbound docking of rigid molecules
-
R. Guigo, D. Gusfield, & H.D. Belitz. Rome: Lecture Notes in Computer Science
-
Duhovny D., Nussinov R., Wolfson H.J. Efficient unbound docking of rigid molecules. Guigo R., Gusfield D., Belitz H.D. Proceedings of the Second Workshop on Algorithms in Bioinformatics, 2452 (WABI). 2002;185-200 Lecture Notes in Computer Science, Rome
-
(2002)
Proceedings of the Second Workshop on Algorithms in Bioinformatics, 2452 (WABI)
, pp. 185-200
-
-
Duhovny, D.1
Nussinov, R.2
Wolfson, H.J.3
-
12
-
-
0037422589
-
Insufficiently dehydrated hydrogen bonds as determinants of protein interactions
-
Fernandez A., Scheraga H.A. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc. Natl. Acad. Sci. USA. 100:2003;113-118
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 113-118
-
-
Fernandez, A.1
Scheraga, H.A.2
-
13
-
-
2542445427
-
ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
-
Glaser F., Pupko T., Paz I., Bell R.E., Bechor-Shental D., Martz E., Ben-Tal N. ConSurf. identification of functional regions in proteins by surface-mapping of phylogenetic information Bioinformatics. 19:2003;163-164
-
(2003)
Bioinformatics
, vol.19
, 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
-
14
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois R., Nielsen J.E., Serrano L. Predicting changes in the stability of proteins and protein complexes. a study of more than 1000 mutations J. Mol. Biol. 320:2002;369-387
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
15
-
-
0036606483
-
Principles of docking: An overview of seach algorithms and a guide to scoring functions
-
Halperin I., Ma B., Wolfson H., Nussinov R. Principles of docking. an overview of seach algorithms and a guide to scoring functions Proteins. 47:2002;409-443
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
16
-
-
0028204490
-
Do salt bridges stabilize proteins? a continuum electrostatic analysis
-
Hendsch Z.S., Tidor B. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3:1994;211-226
-
(1994)
Protein Sci.
, vol.3
, pp. 211-226
-
-
Hendsch, Z.S.1
Tidor, B.2
-
17
-
-
0034213559
-
Conservation of polar residues as hot spots at protein interfaces
-
Hu Z., Ma B., Wolfson H., Nussinov R. Conservation of polar residues as hot spots at protein interfaces. Proteins. 39:2000;331-342
-
(2000)
Proteins
, vol.39
, pp. 331-342
-
-
Hu, Z.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
18
-
-
0025123333
-
The structure of protein-protein recognition sites
-
Janin J., Chothia C. The structure of protein-protein recognition sites. J. Biol. Chem. 256:1990;16027-16030
-
(1990)
J. Biol. Chem.
, vol.256
, pp. 16027-16030
-
-
Janin, J.1
Chothia, C.2
-
20
-
-
1842507022
-
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
-
Keskin O., Tsai C.J., Wolfson H., Nussinov R. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci. 13:2004;1043-1055
-
(2004)
Protein Sci.
, vol.13
, pp. 1043-1055
-
-
Keskin, O.1
Tsai, C.J.2
Wolfson, H.3
Nussinov, R.4
-
21
-
-
0026079134
-
Distribution and complementarity of hyropathy in mulisubunit proteins
-
Korn A.P., Burnett R.M. Distribution and complementarity of hyropathy in mulisubunit proteins. Proteins. 9:1991;37-55
-
(1991)
Proteins
, vol.9
, pp. 37-55
-
-
Korn, A.P.1
Burnett, R.M.2
-
22
-
-
0037195144
-
A simple physical model for binding energy hot spots in protein-protein complexes
-
Kortemme T., Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. USA. 99:2002;14116-14121
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 14116-14121
-
-
Kortemme, T.1
Baker, D.2
-
23
-
-
0035476687
-
Structural basis for the high-affinity interaction of nidogen-1 with immunoglobulin-like domain 3 of perlecan
-
Kvansakul M., Hopf M., Ries A., Timpl R., Hohenester E. Structural basis for the high-affinity interaction of nidogen-1 with immunoglobulin-like domain 3 of perlecan. EMBO J. 19:2001;5342-5346
-
(2001)
EMBO J.
, vol.19
, pp. 5342-5346
-
-
Kvansakul, M.1
Hopf, M.2
Ries, A.3
Timpl, R.4
Hohenester, E.5
-
25
-
-
0028224689
-
Modeling compact denatured states of proteins
-
Lattman E.E., Fiebig K.M., Dill K.A. Modeling compact denatured states of proteins. Biochemistry. 33:1994;6158-6166
-
(1994)
Biochemistry
, vol.33
, pp. 6158-6166
-
-
Lattman, E.E.1
Fiebig, K.M.2
Dill, K.A.3
-
26
-
-
0036468670
-
Evolutionary predictions of binding surfaces and interactions
-
Lichtarge O., Sowa M.E. Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Struct. Biol. 12:2001;21-27
-
(2001)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 21-27
-
-
Lichtarge, O.1
Sowa, M.E.2
-
27
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O., Bourne H.R., Cohen F.E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257:1996;342-358
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
28
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
LoConte L., Chothia C., Janin J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285:1999;2177-2198
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 2177-2198
-
-
Loconte, L.1
Chothia, C.2
Janin, J.3
-
29
-
-
0037340493
-
Development of unified statistical potentials describing protein-protein interactions
-
Lu H., Lu L., Skolnick J. Development of unified statistical potentials describing protein-protein interactions. Biophys. J. 84:2003;1895-1901
-
(2003)
Biophys. J.
, vol.84
, pp. 1895-1901
-
-
Lu, H.1
Lu, L.2
Skolnick, J.3
-
30
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
-
Ma B., Shatsky M., Wolfson H., Nussinov R. Multiple diverse ligands binding at a single protein site. a matter of pre-existing populations Protein Sci. 11:2002;184-197
-
(2002)
Protein Sci.
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.3
Nussinov, R.4
-
31
-
-
0037609791
-
Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
-
Ma B., Elkayam T., Wolfson H.J., Nussinov R. Protein-protein interactions. structurally conserved residues distinguish between binding sites and exposed protein surfaces Proc. Natl. Acad. Sci. USA. 100:2003;5772-5777
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 5772-5777
-
-
Ma, B.1
Elkayam, T.2
Wolfson, H.J.3
Nussinov, R.4
-
32
-
-
0031867090
-
A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies
-
Michnick S.W., Shakhnovich E. A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies. Fold. Des. 3:1998;239-251
-
(1998)
Fold. Des.
, vol.3
, pp. 239-251
-
-
Michnick, S.W.1
Shakhnovich, E.2
-
33
-
-
0035957514
-
Evolutionary conservation of the folding nucleus
-
Mirny L., Shakhnovich E. Evolutionary conservation of the folding nucleus. J. Mol. Biol. 308:2001;123-129
-
(2001)
J. Mol. Biol.
, vol.308
, pp. 123-129
-
-
Mirny, L.1
Shakhnovich, E.2
-
34
-
-
0034769223
-
Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis
-
Norel R., Sheinerman F.B., Petry D., Honig B. Electrostatic contributions to protein-protein interactions. fast energetic filters for docking and their physical basis Protein Sci. 10:2001;2147-2161
-
(2001)
Protein Sci.
, vol.10
, pp. 2147-2161
-
-
Norel, R.1
Sheinerman, F.B.2
Petry, D.3
Honig, B.4
-
35
-
-
0025719208
-
Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques
-
Nussinov R., Wolfson H. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc. Natl. Acad. Sci. USA. 88:1991;10495-10499
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 10495-10499
-
-
Nussinov, R.1
Wolfson, H.2
-
36
-
-
0037229456
-
Analyzing six types of protein-protein interfaces
-
Ofran Y., Rost B. Analyzing six types of protein-protein interfaces. J. Mol. Biol. 325:2003;377-387
-
(2003)
J. Mol. Biol.
, vol.325
, pp. 377-387
-
-
Ofran, Y.1
Rost, B.2
-
37
-
-
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 R.E., Mayrose I., Glaser F., Ben-Tal N. Rate4Site. an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues ISMB. 71:2002;71-77
-
(2002)
ISMB
, vol.71
, pp. 71-77
-
-
Pupko, T.1
Bell, R.E.2
Mayrose, I.3
Glaser, F.4
Ben-Tal, N.5
-
39
-
-
2942629753
-
A method for simultaneous alignment of multiple protein structures
-
Shatsky M., Wolfson H.J., Nussinov R. A method for simultaneous alignment of multiple protein structures. Proteins. in press:2004
-
(2004)
Proteins
-
-
Shatsky, M.1
Wolfson, H.J.2
Nussinov, R.3
-
42
-
-
0035066602
-
ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions
-
Thorn K.S., Bogan A.A. ASEdb. a database of alanine mutations and their effects on the free energy of binding in protein interactions Bioinformatics. 17:2001;284-285
-
(2001)
Bioinformatics
, vol.17
, pp. 284-285
-
-
Thorn, K.S.1
Bogan, A.A.2
-
43
-
-
0030602896
-
A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
-
Tsai C.J., Lin S.L., Wolfson H.J., Nussinov R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J. Mol. Biol. 260:1996;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
-
44
-
-
1842405464
-
Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
-
Tsai C.J., Lin S.L., Wolfson H.J., Nussinov R. Studies of protein-protein interfaces. a statistical analysis of the hydrophobic effect Protein Sci. 6:1997;53-64
-
(1997)
Protein Sci.
, vol.6
, pp. 53-64
-
-
Tsai, C.J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
45
-
-
0031868211
-
Protein folding via binding and vice versa
-
Tsai C.J., Xu D., Nussinov R. Protein folding via binding and vice versa. Fold. Des. 3:1998;R71-R80
-
(1998)
Fold. Des.
, vol.3
, pp. 71-R80
-
-
Tsai, C.J.1
Xu, D.2
Nussinov, R.3
-
46
-
-
0035178383
-
Protein-protein interfaces: Analysis of amino acid conservation in homodimers
-
Valdar W.S.J., Thornton J.M. Protein-protein interfaces. analysis of amino acid conservation in homodimers Proteins. 42:2001;108-124
-
(2001)
Proteins
, vol.42
, pp. 108-124
-
-
Valdar, W.S.J.1
Thornton, J.M.2
-
47
-
-
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. 20:1994;320-329
-
(1994)
Proteins
, vol.20
, pp. 320-329
-
-
Vakser, I.A.1
Aflalo, C.2
-
48
-
-
0036601150
-
Computational methods for prediction of protein interactions
-
Valencia A., Pazos F. Computational methods for prediction of protein interactions. Curr. Opin. Struct. Biol. 12:2002;368-373
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 368-373
-
-
Valencia, A.1
Pazos, F.2
-
49
-
-
0029564595
-
Are buried salt bridges important for protein stability and conformational specificity?
-
Waldburger C.D., Schildbach J.F., Sauer R.T. Are buried salt bridges important for protein stability and conformational specificity? Nat. Struct. Biol. 2:1995;122-128
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 122-128
-
-
Waldburger, C.D.1
Schildbach, J.F.2
Sauer, R.T.3
-
50
-
-
0031893269
-
The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect
-
Xu J., Baase W.A., Baldwin E., Matthews B.W. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Protein Sci. 7:1998;158-177
-
(1998)
Protein Sci.
, vol.7
, pp. 158-177
-
-
Xu, J.1
Baase, W.A.2
Baldwin, E.3
Matthews, B.W.4
-
51
-
-
0037423759
-
An accurate, sensitive, and scalable method to identify functional sites in protein structures
-
Yao H., Kristensen D.M., Mihalek I., Sowa M.E., Shaw C., Kimmel M., Kavraki L., Lichtarge O. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J. Mol. Biol. 326:2003;255-261
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 255-261
-
-
Yao, H.1
Kristensen, D.M.2
Mihalek, I.3
Sowa, M.E.4
Shaw, C.5
Kimmel, M.6
Kavraki, L.7
Lichtarge, O.8
-
52
-
-
0028332007
-
A role for surface hydrophobicity in protein-protein recognition
-
Young L., Jernigan R.L., Covell D.G. A role for surface hydrophobicity in protein-protein recognition. Protein Sci. 3:1994;717-729
-
(1994)
Protein Sci.
, vol.3
, pp. 717-729
-
-
Young, L.1
Jernigan, R.L.2
Covell, D.G.3
-
54
-
-
0023660653
-
Prediction of protein secondary structure and active sites using the alignment of homologous sequences
-
Zvelebil M.J., Barton G.J., Taylor W.R., Sternberg M.J. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J. Mol. Biol. 195:1987;957-961
-
(1987)
J. Mol. Biol.
, vol.195
, pp. 957-961
-
-
Zvelebil, M.J.1
Barton, G.J.2
Taylor, W.R.3
Sternberg, M.J.4
|