-
1
-
-
0033971642
-
DIP: The database of interacting proteins
-
Xenarios, I., Rice, D. W., Salwinski, L., Baron, M. K., Marcotte, E. M. & Eisenberg, D. (2000). DIP: The database of interacting proteins. Nucl. Acids Res. 28, 289-291.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 289-291
-
-
Xenarios, I.1
Rice, D.W.2
Salwinski, L.3
Baron, M.K.4
Marcotte, E.M.5
Eisenberg, D.6
-
2
-
-
0017751668
-
The Protein Data Bank. A computer-based archival file for macromolecular structures
-
Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. F., Jr, Brice, M. D., Rodgers, J. R. et al. (1977). The Protein Data Bank. A computer-based archival file for macromolecular structures. Eur. J. Biochem. 80, 319-324.
-
(1977)
Eur. J. Biochem.
, vol.80
, pp. 319-324
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.3
Meyer E.F., Jr.4
Brice, M.D.5
Rodgers, J.R.6
-
3
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., Westbrook, J., Feng, Z., Gillliland, G., Bhat, T. N., Weissig, H. et al. (2000). The Protein Data Bank. Nucl. Acids Res. 28, 235-242.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gillliland, G.4
Bhat, T.N.5
Weissig, H.6
-
4
-
-
0033957834
-
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
-
Bairoch, A. & Apweiler, R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucl. Acids Res. 28, 45-48.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 45-48
-
-
Bairoch, A.1
Apweiler, R.2
-
5
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones, S. & Thornton, J. M. (1996). Principles of protein-protein interactions. Proc. Natl Acad. Sci. USA, 93, 13-20.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 13-20
-
-
Jones, S.1
Thornton, J.M.2
-
6
-
-
0031565729
-
Analysis of protein-protein interaction sites using surface patches
-
Jones, S. & Thornton, J. M. (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
-
-
Jones, S.1
Thornton, J.M.2
-
7
-
-
0031678069
-
Empirical solvent-mediated potentials hold for both intra-molecular and intermolecular inter-residue interactions
-
Keskin, O., Bahar, I., Badretdinov, A. Y., Ptitsyn, O. B. & Jernigan, R. L. (1998). Empirical solvent-mediated potentials hold for both intra-molecular and intermolecular 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
-
8
-
-
0035342450
-
Residue frequencies and pairing preferences at protein-protein interfaces
-
Glaser, F., Steinberg, D. M., Vakser, I. A. & Ben-Tal, N. (2001). Residue frequencies and pairing preferences at protein-protein interfaces. Proteins: Struct. Funct. Genet. 43, 89-102.
-
(2001)
Proteins: Struct. Funct. Genet.
, vol.43
, pp. 89-102
-
-
Glaser, F.1
Steinberg, D.M.2
Vakser, I.A.3
Ben-Tal, N.4
-
9
-
-
0031547966
-
Electrostatic complementarity at protein/protein interfaces
-
McCoy, A. J., Chandana Epa, V. & Colman, P. M. (1997). Electrostatic complementarity at protein/protein interfaces. J. Mol. Biol. 268, 570-584.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 570-584
-
-
McCoy, A.J.1
Chandana Epa, V.2
Colman, P.M.3
-
10
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo Conte, L., Chothia, C. & 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
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
11
-
-
0034039797
-
Electrostatic aspects of protein-protein interactions
-
Sheinerman, F. B., Norel, R. & Honig, B. (2000). Electrostatic aspects of protein-protein interactions. Curr. Opin. Struct. Biol. 10, 153-159.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 153-159
-
-
Sheinerman, F.B.1
Norel, R.2
Honig, B.3
-
12
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan, A. A. & 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
-
13
-
-
0034060520
-
Protein domain interfaces: Characterization and comparison with oligomeric protein interfaces
-
Jones, S., Marin, A. & Thornton, J. M. (2000). Protein domain interfaces: Characterization and comparison with oligomeric protein interfaces. Protein Eng. 13, 77-82.
-
(2000)
Protein Eng
, vol.13
, pp. 77-82
-
-
Jones, S.1
Marin, A.2
Thornton, J.M.3
-
14
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. & Sakaki, Y. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
15
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R. et al. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
-
16
-
-
0029942661
-
Structure-derived potentials and protein simulations
-
Jernigan, R. L. & Bahar, I. (1996). Structure-derived potentials and protein simulations. J. Mol. Biol. 6, 195-209.
-
(1996)
J. Mol. Biol.
, vol.6
, pp. 195-209
-
-
Jernigan, R.L.1
Bahar, I.2
-
17
-
-
0031566950
-
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
-
Bahar, I. & Jernigan, R. L. (1997). Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266, 195-214.
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 195-214
-
-
Bahar, I.1
Jernigan, R.L.2
-
18
-
-
0029942661
-
Structure-derived potentials and protein simulations
-
Bahar, I. & Jernigan, R. L. (1996). Structure-derived potentials and protein simulations. J. Mol. Biol. 6, 195-209.
-
(1996)
J. Mol. Biol.
, vol.6
, pp. 195-209
-
-
Bahar, I.1
Jernigan, R.L.2
-
19
-
-
0033020656
-
GRASS: A server for the graphical representation and analysis of structures
-
Nayal, M., Hitz, B. C. & Honig, B. (1999). GRASS: A server for the graphical representation and analysis of structures. Protein Sci. 8, 676-679.
-
(1999)
Protein Sci.
, vol.8
, pp. 676-679
-
-
Nayal, M.1
Hitz, B.C.2
Honig, B.3
-
20
-
-
0035059281
-
Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?
-
Fetrow, J. S., Siew, N., Di Gennaro, J. A., Martinez-Yamout, M., Dyson, H. J. & Skolnick, J. (2001). Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight? Protein Sci. 10, 1005-1014.
-
(2001)
Protein Sci.
, vol.10
, pp. 1005-1014
-
-
Fetrow, J.S.1
Siew, N.2
Di Gennaro, J.A.3
Martinez-Yamout, M.4
Dyson, H.J.5
Skolnick, J.6
-
21
-
-
0001689602
-
The effect of sample size on the meaning of significance tests
-
Royall, R. M. (1986). The effect of sample size on the meaning of significance tests. The American Statistician, 40, 313-315.
-
(1986)
The American Statistician
, vol.40
, pp. 313-315
-
-
Royall, R.M.1
-
22
-
-
0031561809
-
Protein binding versus protein folding: The role of hydrophilic bridges in protein associations
-
Xu, D., Lin, S. L. & Nussinov, R. (1997). Protein binding versus protein folding: The role of hydrophilic bridges in protein associations. J. Mol. Biol. 265, 68-84.
-
(1997)
J. Mol. Biol.
, vol.265
, pp. 68-84
-
-
Xu, D.1
Lin, S.L.2
Nussinov, R.3
-
23
-
-
0035882570
-
Prediction of protein interaction sites from sequence profile and residue neighbor list
-
Zhou, H. X. & Shan, Y. (2001). Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins: Struct. Funct. Genet. 44, 336-343.
-
(2001)
Proteins: Struct. Funct. Genet.
, vol.44
, pp. 336-343
-
-
Zhou, H.X.1
Shan, Y.2
-
25
-
-
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., Flöckner, H., Froschauer, R., Gottsbacher, K. et al. (1990). 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. 216, 167-180.
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Flöckner, H.4
Froschauer, R.5
Gottsbacher, K.6
-
26
-
-
0033835533
-
Structure-derived substitution matrices for alignment of distantly related sequences
-
Prlic, A., Domingues, F. S. & Sippl, M. J. (2000). Structure-derived substitution matrices for alignment of distantly related sequences. Protein Eng. 13, 545-550.
-
(2000)
Protein Eng.
, vol.13
, pp. 545-550
-
-
Prlic, A.1
Domingues, F.S.2
Sippl, M.J.3
-
27
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl, M. J. (1995). Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5, 229-235.
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
28
-
-
0033562633
-
Use of pair potentials across protein interfaces in screening predicted docked complexes
-
Moont, G., Gabb, H. A. & Sternberg, M. J. (1999). Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins: Struct. Funct. Genet. 35, 364-373.
-
(1999)
Proteins: Struct. Funct. Genet.
, vol.35
, pp. 364-373
-
-
Moont, G.1
Gabb, H.A.2
Sternberg, M.J.3
-
29
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy, P. & Russell, R. B. (2002). Interrogating protein interaction networks through structural biology. Proc. Natl Acad. Sci. USA, 99, 5896-5901.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
30
-
-
0035838976
-
Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
-
Aloy, P., Querol, E., Aviles, F. X. & Sternberg, M. J. (2001). Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol. 311, 395-408.
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 395-408
-
-
Aloy, P.1
Querol, E.2
Aviles, F.X.3
Sternberg, M.J.4
-
31
-
-
0033410193
-
Structural determinants of trypsin affinity and specificity for cationic inhibitors
-
Polticelli, F., Ascenzi, P., Bolognesi, M. & Honig, B. (1999). Structural determinants of trypsin affinity and specificity for cationic inhibitors. Protein Sci. 8, 2621-2629.
-
(1999)
Protein Sci.
, vol.8
, pp. 2621-2629
-
-
Polticelli, F.1
Ascenzi, P.2
Bolognesi, M.3
Honig, B.4
-
32
-
-
0028958462
-
Conservation of salt bridges in protein families
-
Schueler, O. & Margalit, H. (1995). Conservation of salt bridges in protein families. J. Mol. Biol. 248, 125-135.
-
(1995)
J. Mol. Biol.
, vol.248
, pp. 125-135
-
-
Schueler, O.1
Margalit, H.2
-
33
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B. & Nicholls, A. (1995). Classical electrostatics in biology and chemistry. Science, 268, 1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
34
-
-
0031565725
-
Prediction of protein-protein interaction sites using patch analysis
-
Jones, S. & Thornton, J. M. (1997). Prediction of protein-protein interaction sites using patch analysis. J. Mol. Biol. 272, 133-143.
-
(1997)
J. Mol. Biol.
, vol.272
, pp. 133-143
-
-
Jones, S.1
Thornton, J.M.2
-
35
-
-
0036308741
-
Enzyme function less conserved than anticipated
-
Rost, B. (2002). Enzyme function less conserved than anticipated. J. Mol. Biol. 318, 595-608.
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 595-608
-
-
Rost, B.1
-
36
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost, B. (1999). Twilight zone of protein sequence alignments. Protein Eng. 12, 85-94.
-
(1999)
Protein Eng.
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
37
-
-
0032169688
-
PQS: A protein quaternary structure file server
-
Henrick, K. & Thornton, J. M. (1998). PQS: A protein quaternary structure file server. Trends Biochem. Sci. 23, 358-361.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 358-361
-
-
Henrick, K.1
Thornton, J.M.2
-
38
-
-
0035853028
-
Identification of protein oligomerization states by analysis of interface conservation
-
Elcock, A. H. & McCammon, J. A. (2001). Identification of protein oligomerization states by analysis of interface conservation. Proc. Natl Acad. Sci. USA, 98, 2990-2994.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 2990-2994
-
-
Elcock, A.H.1
McCammon, J.A.2
-
39
-
-
0030581603
-
Bootstrap confidence levels for phylogenetic trees
-
Efron, B., Halloran, E. & Holmes, S. (1996). Bootstrap confidence levels for phylogenetic trees. Proc. Natl Acad. Sci. USA, 93, 13429-13434.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 13429-13434
-
-
Efron, B.1
Halloran, E.2
Holmes, S.3
-
40
-
-
0025952277
-
Divergence measures based on the Shannon entropy
-
Lin, J. (1991). Divergence measures based on the Shannon entropy. IEEE Trans. Inform. Theory, 37, 145-151.
-
(1991)
IEEE Trans. Inform. Theory
, vol.37
, pp. 145-151
-
-
Lin, J.1
-
41
-
-
84940644968
-
A mathematical theory of communication
-
see also pp. 623-656
-
Shannon, C. E. (1948). A mathematical theory of communication. Bell System Tech. J. 27, 379-423; see also pp. 623-656.
-
(1948)
Bell System Tech. J.
, vol.27
, pp. 379-423
-
-
Shannon, C.E.1
-
42
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte, J. & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
43
-
-
0034682881
-
An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance
-
Yang, A. S. & Honig, B. (2000). An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J. Mol. Biol. 301, 665-678.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 665-678
-
-
Yang, A.S.1
Honig, B.2
-
44
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
45
-
-
0028300741
-
Combining evolutionary information and neural networks to predict protein secondary structure
-
Rost, B. & Sander, C. (1994). Combining evolutionary information and neural networks to predict protein secondary structure. Proteins: Struct. Funct. Genet. 19, 55-72.
-
(1994)
Proteins: Struct. Funct. Genet.
, vol.19
, pp. 55-72
-
-
Rost, B.1
Sander, C.2
|