-
1
-
-
0016708122
-
Principles of protein-protein recognition
-
Chothia C, Janin J. Principles of protein-protein recognition. Nature 1975;256:705-708.
-
(1975)
Nature
, vol.256
, pp. 705-708
-
-
Chothia, C.1
Janin, J.2
-
2
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996;93:13-20.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 13-20
-
-
Jones, S.1
Thornton, J.M.2
-
3
-
-
1042275583
-
A dissection of specific and non-specific protein-protein interfaces
-
Bahadur RP, Chakrabarti P, Rodier F, Janin J. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 2004;336:943-955.
-
(2004)
J Mol Biol
, vol.336
, pp. 943-955
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
Janin, J.4
-
4
-
-
0037093645
-
Dissecting protein-protein recognition sites
-
Chakrabarti P, Janin J. Dissecting protein-protein recognition sites. Proteins 2002;47:334-343.
-
(2002)
Proteins
, vol.47
, pp. 334-343
-
-
Chakrabarti, P.1
Janin, J.2
-
5
-
-
0029988383
-
Protein-protein interfaces: Architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences
-
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Crit Rev Biochem Mol Biol 1996;31:127-152.
-
(1996)
Crit Rev Biochem Mol Biol
, vol.31
, pp. 127-152
-
-
Tsai, C.J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
6
-
-
0035178383
-
Protein-protein interfaces: Analysis of amino acid conservation in homodimers
-
Valdar WS, Thornton JM. Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 2001;42:108-124.
-
(2001)
Proteins
, vol.42
, pp. 108-124
-
-
Valdar, W.S.1
Thornton, J.M.2
-
7
-
-
0031561809
-
Protein binding versus protein folding: The role of hydrophilic bridges in protein associations
-
Xu D, Lin SL, Nussinov R. Protein binding versus protein folding: the role of hydrophilic bridges in protein associations. J Mol Biol 1997;265:68-84.
-
(1997)
J Mol Biol
, vol.265
, pp. 68-84
-
-
Xu, D.1
Lin, S.L.2
Nussinov, R.3
-
8
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;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
-
9
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
-
(1999)
J Mol Biol
, vol.285
, pp. 2177-2198
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
11
-
-
0034308172
-
Discriminating between homodimeric and monomelic proteins in the crystalline state
-
Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomelic proteins in the crystalline state. Proteins 2000;41:47-57.
-
(2000)
Proteins
, vol.41
, pp. 47-57
-
-
Ponstingl, H.1
Henrick, K.2
Thornton, J.M.3
-
12
-
-
0030877077
-
Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers
-
Dasgupta S, Iyer GH, Bryant SH, Lawrence CE, Bell JA. Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins 1997;28:494-514.
-
(1997)
Proteins
, vol.28
, pp. 494-514
-
-
Dasgupta, S.1
Iyer, G.H.2
Bryant, S.H.3
Lawrence, C.E.4
Bell, J.A.5
-
14
-
-
0023155210
-
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 1987;193:775-791.
-
(1987)
J Mol Biol
, vol.193
, pp. 775-791
-
-
Ponder, J.W.1
Richards, F.M.2
-
15
-
-
28644448657
-
Survey of the geometric association of domain-domain interfaces
-
Kim WK, Ison JC. Survey of the geometric association of domain-domain interfaces. Proteins 2005;61:1075-1088.
-
(2005)
Proteins
, vol.61
, pp. 1075-1088
-
-
Kim, W.K.1
Ison, J.C.2
-
16
-
-
0026079134
-
Distribution and complementarity of hydropathy in multisubunit proteins
-
Korn AP, Burnett RM. Distribution and complementarity of hydropathy in multisubunit proteins. Proteins 1991;9:37-55.
-
(1991)
Proteins
, vol.9
, pp. 37-55
-
-
Korn, A.P.1
Burnett, R.M.2
-
17
-
-
0028332007
-
A role for surface hydrophobicity in protein-protein recognition
-
Young L, Jernigan RL, Covell DG. A role for surface hydrophobicity in protein-protein recognition. Protein Sci 1994;3:717-729.
-
(1994)
Protein Sci
, vol.3
, pp. 717-729
-
-
Young, L.1
Jernigan, R.L.2
Covell, D.G.3
-
18
-
-
0030997363
-
Hydrophobic patches on protein subunit interfaces: Characteristics and prediction
-
Lijnzaad P, Argos P. Hydrophobic patches on protein subunit interfaces: characteristics and prediction. Proteins 1997;28:333-343.
-
(1997)
Proteins
, vol.28
, pp. 333-343
-
-
Lijnzaad, P.1
Argos, P.2
-
19
-
-
0031454652
-
Simulating the minimum core for hydrophobic collapse in globular proteins
-
Tsai J, Gerstein M, Levitt M. Simulating the minimum core for hydrophobic collapse in globular proteins. Protein Sci 1997;6:2606-2616.
-
(1997)
Protein Sci
, vol.6
, pp. 2606-2616
-
-
Tsai, J.1
Gerstein, M.2
Levitt, M.3
-
20
-
-
0028607523
-
Cavities and packing at protein interfaces
-
Hubbard SJ, Argos P. Cavities and packing at protein interfaces. Protein Sci 1994;3:2194-2206.
-
(1994)
Protein Sci
, vol.3
, pp. 2194-2206
-
-
Hubbard, S.J.1
Argos, P.2
-
21
-
-
0024046505
-
An investigation of protein subunit and domain interfaces
-
Argos P. An investigation of protein subunit and domain interfaces. Protein Eng 1988;2:101-113.
-
(1988)
Protein Eng
, vol.2
, pp. 101-113
-
-
Argos, P.1
-
23
-
-
0024246956
-
Surface, subunit interfaces and interior of oligomeric proteins
-
Janin J, Miller S, Chothia C. Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol 1988;204:155-164.
-
(1988)
J Mol Biol
, vol.204
, pp. 155-164
-
-
Janin, J.1
Miller, S.2
Chothia, C.3
-
24
-
-
0035970298
-
Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast
-
Park J, Lappe M, Teichmann SA. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol 2001;307:929-938.
-
(2001)
J Mol Biol
, vol.307
, pp. 929-938
-
-
Park, J.1
Lappe, M.2
Teichmann, S.A.3
-
25
-
-
0042386609
-
The relationship between sequence and interaction divergence in proteins
-
Aloy P, Ceulemans H, Stark A, Russell RB. The relationship between sequence and interaction divergence in proteins. J Mol Biol 2003;332:989-998.
-
(2003)
J Mol Biol
, vol.332
, pp. 989-998
-
-
Aloy, P.1
Ceulemans, H.2
Stark, A.3
Russell, R.B.4
-
26
-
-
1842507022
-
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
-
Keskin O, Tsai CJ, Wolfson H, Nussinov R. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci 2004;13:1043-1055.
-
(2004)
Protein Sci
, vol.13
, pp. 1043-1055
-
-
Keskin, O.1
Tsai, C.J.2
Wolfson, H.3
Nussinov, R.4
-
27
-
-
0030602896
-
A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
-
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol 1996;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
-
28
-
-
26444568633
-
Statistical analysis of predominantly transient protein-protein interfaces
-
Ansari S, Helms V. Statistical analysis of predominantly transient protein-protein interfaces. Proteins 2005;61:344-355.
-
(2005)
Proteins
, vol.61
, pp. 344-355
-
-
Ansari, S.1
Helms, V.2
-
29
-
-
0031678069
-
Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions
-
Keskin O, Bahar I, Badretdinov AY, Ptitsyn OB, Jernigan RL. Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Sci 1998;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
-
30
-
-
0031566950
-
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
-
Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 1997;266:195-214.
-
(1997)
J Mol Biol
, vol.266
, pp. 195-214
-
-
Bahar, I.1
Jernigan, R.L.2
-
31
-
-
0025008445
-
Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
-
Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J Mol Biol 1990;216:167-180.
-
(1990)
J Mol Biol
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Floeckner, H.4
Froschauer, R.5
Gottsbacher, K.6
Casari, G.7
Sippl, M.J.8
-
32
-
-
0033835533
-
Structure-derived substitution matrices for alignment of distantly related sequences
-
Prlic A, Domingues FS, Sippl MJ. Structure-derived substitution matrices for alignment of distantly related sequences. Protein Eng 2000;13:545-550.
-
(2000)
Protein Eng
, vol.13
, pp. 545-550
-
-
Prlic, A.1
Domingues, F.S.2
Sippl, M.J.3
-
33
-
-
0035342450
-
Residue frequencies and pairing preferences at protein-protein interfaces
-
Glaser F, Steinberg DM, Vakser IA, Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 2001;43:89-102.
-
(2001)
Proteins
, vol.43
, pp. 89-102
-
-
Glaser, F.1
Steinberg, D.M.2
Vakser, I.A.3
Ben-Tal, N.4
-
34
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy P, Russell RB. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 2002;99:5896-5901.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
35
-
-
0029089271
-
Significance of bound water to local chain conformations in protein crystals
-
Robert CH, Ho PS. Significance of bound water to local chain conformations in protein crystals. Proc Natl Acad Sci USA 1995;92:7600-7604.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 7600-7604
-
-
Robert, C.H.1
Ho, P.S.2
-
36
-
-
0015977588
-
The interpretation of protein structures: Total volume, group volume distributions and packing density
-
Richards FM. The interpretation of protein structures: total volume, group volume distributions and packing density. J Mol Biol 1974;82:1-14.
-
(1974)
J Mol Biol
, vol.82
, pp. 1-14
-
-
Richards, F.M.1
-
37
-
-
1842850600
-
Voronoi and Voronoi-related tessellations in studies of protein structure and interaction
-
Poupon A. Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. Curr Opin Struct Biol 2004;14:233-241.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 233-241
-
-
Poupon, A.1
-
38
-
-
0034287449
-
Voronoi tessellation reveals the condensed matter character of folded proteins
-
Soyer A, Chomilier J, Mornon JP, Jullien R, Sadoc JF. Voronoi tessellation reveals the condensed matter character of folded proteins. Phys Rev Lett 2000;85:3532-3535.
-
(2000)
Phys Rev Lett
, vol.85
, pp. 3532-3535
-
-
Soyer, A.1
Chomilier, J.2
Mornon, J.P.3
Jullien, R.4
Sadoc, J.F.5
-
39
-
-
0036892439
-
Nonatomic solvent-driven Voronoi tessellation of proteins: An open tool to analyze protein folds
-
Angelov B, Sadoc JF, Jullien R, Soyer A, Mornon JP, Chomilier J. Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds. Proteins 2002;49:446-456.
-
(2002)
Proteins
, vol.49
, pp. 446-456
-
-
Angelov, B.1
Sadoc, J.F.2
Jullien, R.3
Soyer, A.4
Mornon, J.P.5
Chomilier, J.6
-
40
-
-
0029004611
-
The volume of atoms on the protein surface: Calculated from simulation, using Voronoi polyhedra
-
Gerstein M, Tsai J, Levitt M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J Mol Biol 1995;249:955-966.
-
(1995)
J Mol Biol
, vol.249
, pp. 955-966
-
-
Gerstein, M.1
Tsai, J.2
Levitt, M.3
-
41
-
-
0006166868
-
Structure characterization and predictability by Voronoi analysis
-
Christensen SW, Thomas NW. Structure characterization and predictability by Voronoi analysis. Acta Crystallogr A 1999;55(Part 5):811-820.
-
(1999)
Acta Crystallogr A
, vol.55
, Issue.PART 5
, pp. 811-820
-
-
Christensen, S.W.1
Thomas, N.W.2
-
43
-
-
0034778102
-
Determining the minimum number of types necessary to represent the sizes of protein atoms
-
Tsai J, Voss N, Gerstein M. Determining the minimum number of types necessary to represent the sizes of protein atoms. Bioinformatics 2001;17:949-956.
-
(2001)
Bioinformatics
, vol.17
, pp. 949-956
-
-
Tsai, J.1
Voss, N.2
Gerstein, M.3
-
45
-
-
24344487344
-
Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions
-
Mintz S, Shulman-Peleg A, Wolfson HJ, Nussinov R. Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions. Proteins 2005;61:6-20.
-
(2005)
Proteins
, vol.61
, pp. 6-20
-
-
Mintz, S.1
Shulman-Peleg, A.2
Wolfson, H.J.3
Nussinov, R.4
-
46
-
-
0025272240
-
Rapid and sensitive sequence comparison with FASTP and FASTA
-
Pearson WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 1990;183:63-98.
-
(1990)
Methods Enzymol
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
-
47
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992;8:275-282.
-
(1992)
Comput Appl Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
48
-
-
26844500695
-
Interresidue contacts in proteins and protein-protein interfaces and their use in characterizing the homodimeric interface
-
Saha RP, Bahadur RP, Chakrabarti P. Interresidue contacts in proteins and protein-protein interfaces and their use in characterizing the homodimeric interface. J Proteome Res 2005;4:1600-1609.
-
(2005)
J Proteome Res
, vol.4
, pp. 1600-1609
-
-
Saha, R.P.1
Bahadur, R.P.2
Chakrabarti, P.3
-
49
-
-
34248529053
-
-
Kendall M, Stuart A. Kendall's advanced theory of statistics. Arnold, London 2A Classical Inference and the linear Model. 6 th edition. 1998.
-
Kendall M, Stuart A. Kendall's advanced theory of statistics. Arnold, London Volume 2A Classical Inference and the linear Model. 6 th edition. 1998.
-
-
-
-
50
-
-
29344461522
-
Breaking symmetry in protein dimers: Designs and functions
-
Brown JH. Breaking symmetry in protein dimers: designs and functions. Protein Sci 2006;15:1-13.
-
(2006)
Protein Sci
, vol.15
, pp. 1-13
-
-
Brown, J.H.1
-
51
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
52
-
-
30544438396
-
The analysis of multiprotein complexes: The yeast and the human spliceosome as case studies
-
Neubauer G. The analysis of multiprotein complexes: the yeast and the human spliceosome as case studies. Methods Enzymol 2005;405:236-263.
-
(2005)
Methods Enzymol
, vol.405
, pp. 236-263
-
-
Neubauer, G.1
-
53
-
-
16644386648
-
The importance of disulfide bridging
-
Swaisgood HE. The importance of disulfide bridging. Biotechnol Adv 2005;23:71-73.
-
(2005)
Biotechnol Adv
, vol.23
, pp. 71-73
-
-
Swaisgood, H.E.1
|