-
1
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., and Ignatchenko A. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 440 2006 637 643
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
Ignatchenko, A.6
-
2
-
-
0035896024
-
ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
-
Armon A., Graur D., and Ben-Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information J. Mol. Biol. 307 2001 447 463
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 447-463
-
-
Armon, A.1
Graur, D.2
Ben-Tal, N.3
-
3
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O., Bourne H.R., and 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
-
4
-
-
0346733329
-
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
-
Caffrey D.R., Somaroo S., Hughes J.D., Mintseris J., and Huang E.S. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci. 13 2004 190 202
-
(2004)
Protein Sci.
, vol.13
, pp. 190-202
-
-
Caffrey, D.R.1
Somaroo, S.2
Hughes, J.D.3
Mintseris, J.4
Huang, E.S.5
-
5
-
-
34247555940
-
On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues
-
Mihalek I., Res I., and Lichtarge O. On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues J. Mol. Biol. 369 2007 584 595
-
(2007)
J. Mol. Biol.
, vol.369
, pp. 584-595
-
-
Mihalek, I.1
Res, I.2
Lichtarge, O.3
-
6
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris J., and Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions Proc. Natl Acad. Sci. USA 102 2005 10930 10935
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
7
-
-
0028916599
-
A hot spot of binding energy in a hormone-receptor interface
-
Clackson T., and 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
-
8
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan A., and Thorn K. 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.1
Thorn, K.2
-
9
-
-
34547573955
-
Protein-protein interaction hotspots carved into sequences
-
Ofran Y., and Rost B. Protein-protein interaction hotspots carved into sequences PLoS Comput. Biol. 3 2007 e119
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 119
-
-
Ofran, Y.1
Rost, B.2
-
10
-
-
0035882570
-
Prediction of protein interaction sites from sequence profile and residue neighbor list
-
Zhou H.X., and Shan Y. Prediction of protein interaction sites from sequence profile and residue neighbor list Proteins 44 2001 336 343
-
(2001)
Proteins
, vol.44
, pp. 336-343
-
-
Zhou, H.X.1
Shan, Y.2
-
11
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo Conte L., Chothia C., and 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
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
12
-
-
0031565729
-
Analysis of protein-protein interaction sites using surface patches
-
Jones S., and Thornton J.M. Analysis of protein-protein interaction sites using surface patches J. Mol. Biol. 272 1997 121 132
-
(1997)
J. Mol. Biol.
, vol.272
, pp. 121-132
-
-
Jones, S.1
Thornton, J.M.2
-
13
-
-
24344484686
-
Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data
-
Chen H., and Zhou H.X. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data Proteins 61 2005 21 35
-
(2005)
Proteins
, vol.61
, pp. 21-35
-
-
Chen, H.1
Zhou, H.X.2
-
14
-
-
33646122452
-
An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements
-
Hoskins J., Lovell S., and Blundell T.L. An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements Protein Sci. 15 2006 1017 1029
-
(2006)
Protein Sci.
, vol.15
, pp. 1017-1029
-
-
Hoskins, J.1
Lovell, S.2
Blundell, T.L.3
-
15
-
-
1842526090
-
ProMate: A structure based prediction program to identify the location of protein-protein binding sites
-
Neuvirth H., Raz R., and Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites J. Mol. Biol. 338 2004 181 199
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 181-199
-
-
Neuvirth, H.1
Raz, R.2
Schreiber, G.3
-
17
-
-
34548767667
-
Interaction-site prediction for protein complexes: A critical assessment
-
Zhou H.X., and Qin S. Interaction-site prediction for protein complexes: a critical assessment Bioinformatics 23 2007 2203 2209
-
(2007)
Bioinformatics
, vol.23
, pp. 2203-2209
-
-
Zhou, H.X.1
Qin, S.2
-
18
-
-
49249109524
-
How proteins get in touch: Interface prediction in the study of biomolecular complexes
-
de Vries S.J., and Bonvin A.M. How proteins get in touch: interface prediction in the study of biomolecular complexes Curr. Protein Pept. Sci. 9 2008 394 406
-
(2008)
Curr. Protein Pept. Sci.
, vol.9
, pp. 394-406
-
-
De Vries, S.J.1
Bonvin, A.M.2
-
19
-
-
33947360625
-
PIER: Protein interface recognition for structural proteomics
-
Kufareva I., Budagyan L., Raush E., Totrov M., and Abagyan R. PIER: protein interface recognition for structural proteomics Proteins 67 2007 400 417
-
(2007)
Proteins
, vol.67
, pp. 400-417
-
-
Kufareva, I.1
Budagyan, L.2
Raush, E.3
Totrov, M.4
Abagyan, R.5
-
20
-
-
79959593991
-
Characterization of protein-protein interaction interfaces from a single species
-
Talavera D., Robertson D.L., and Lovell S.C. Characterization of protein-protein interaction interfaces from a single species PLoS One 6 2011 e21053
-
(2011)
PLoS One
, vol.6
, pp. 21053
-
-
Talavera, D.1
Robertson, D.L.2
Lovell, S.C.3
-
21
-
-
33646182934
-
An integrated view of protein evolution
-
Pal C., Papp B., and Lercher M.J. An integrated view of protein evolution Nat. Rev. Genet. 7 2006 337 348
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 337-348
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
22
-
-
77958114505
-
An integrated view of molecular coevolution in protein-protein interactions
-
Lovell S.C., and Robertson D.L. An integrated view of molecular coevolution in protein-protein interactions Mol. Biol. Evol. 27 2010 2567 2575
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 2567-2575
-
-
Lovell, S.C.1
Robertson, D.L.2
-
23
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy P., and Russell R.B. Interrogating protein interaction networks through structural biology Proc. Natl Acad. Sci. USA 99 2002 5896 5901
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
24
-
-
74549136698
-
Tradeoff between stability and multispecificity in the design of promiscuous proteins
-
Fromer M., and Shifman J.M. Tradeoff between stability and multispecificity in the design of promiscuous proteins PLoS Comput. Biol. 5 2009 e1000627
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. 1000627
-
-
Fromer, M.1
Shifman, J.M.2
-
25
-
-
79952608525
-
Accurate bond and angle parameters for X-ray protein-structure refinement
-
Engh R.A., and Huber R. Accurate bond and angle parameters for X-ray protein-structure refinement Acta Crystallogr., Sect. A: Found. Crystallogr. 47 1991 392 400
-
(1991)
Acta Crystallogr., Sect. A: Found. Crystallogr.
, vol.47
, pp. 392-400
-
-
Engh, R.A.1
Huber, R.2
-
26
-
-
0034663722
-
The penultimate rotamer library
-
Lovell S.C., Word J.M., Richardson J.S., and Richardson D.C. The penultimate rotamer library Proteins: Struct., Funct., Genet. 40 2000 389 408
-
(2000)
Proteins: Struct., Funct., Genet.
, vol.40
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
27
-
-
0033613812
-
Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms
-
Word J.M., Lovell S.C., LaBean T.H., Taylor H.C., Zalis M.E., and Presley B.K. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms J. Mol. Biol. 285 1999 1711 1733
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1711-1733
-
-
Word, J.M.1
Lovell, S.C.2
Labean, T.H.3
Taylor, H.C.4
Zalis, M.E.5
Presley, B.K.6
-
28
-
-
77949898545
-
The (non)malignancy of cancerous amino acidic substitutions
-
Talavera D., Taylor M.S., and Thornton J.M. The (non)malignancy of cancerous amino acidic substitutions Proteins 78 2010 518 529
-
(2010)
Proteins
, vol.78
, pp. 518-529
-
-
Talavera, D.1
Taylor, M.S.2
Thornton, J.M.3
-
29
-
-
34047232679
-
The (in)dependence of alternative splicing and gene duplication
-
Talavera D., Vogel C., Orozco M., Teichmann S.A., and de la Cruz X. The (in)dependence of alternative splicing and gene duplication PLoS Comput. Biol. 3 2007 e33
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 33
-
-
Talavera, D.1
Vogel, C.2
Orozco, M.3
Teichmann, S.A.4
De La Cruz, X.5
-
30
-
-
0041825432
-
Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes
-
Bleichenbacher M., Tan S., and Richmond T.J. Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes J. Mol. Biol. 332 2003 783 793
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 783-793
-
-
Bleichenbacher, M.1
Tan, S.2
Richmond, T.J.3
-
31
-
-
33646116786
-
Structural and functional organization of the ESCRT-I trafficking complex
-
Kostelansky M.S., Sun J., Lee S., Kim J., Ghirlando R., and Hierro A. Structural and functional organization of the ESCRT-I trafficking complex Cell 125 2006 113 126
-
(2006)
Cell
, vol.125
, pp. 113-126
-
-
Kostelansky, M.S.1
Sun, J.2
Lee, S.3
Kim, J.4
Ghirlando, R.5
Hierro, A.6
-
32
-
-
34250745253
-
Structure and organization of coat proteins in the COPII cage
-
Fath S., Mancias J.D., Bi X., and Goldberg J. Structure and organization of coat proteins in the COPII cage Cell 129 2007 1325 1336
-
(2007)
Cell
, vol.129
, pp. 1325-1336
-
-
Fath, S.1
Mancias, J.D.2
Bi, X.3
Goldberg, J.4
-
33
-
-
0033638335
-
Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Balpha
-
Andersen G.R., Pedersen L., Valente L., Chatterjee I., Kinzy T.G., Kjeldgaard M., and Nyborg J. Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Balpha Mol. Cell 6 2000 1261 1266
-
(2000)
Mol. Cell
, vol.6
, pp. 1261-1266
-
-
Andersen, G.R.1
Pedersen, L.2
Valente, L.3
Chatterjee, I.4
Kinzy, T.G.5
Kjeldgaard, M.6
Nyborg, J.7
-
34
-
-
0042386609
-
The relationship between sequence and interaction divergence in proteins
-
Aloy P., Ceulemans H., Stark A., and Russell R.B. The relationship between sequence and interaction divergence in proteins J. Mol. Biol. 332 2003 989 998
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 989-998
-
-
Aloy, P.1
Ceulemans, H.2
Stark, A.3
Russell, R.B.4
-
35
-
-
12144290243
-
Structure-based assembly of protein complexes in yeast
-
Aloy P., Bottcher B., Ceulemans H., Leutwein C., Mellwig C., and Fischer S. Structure-based assembly of protein complexes in yeast Science 303 2004 2026 2029
-
(2004)
Science
, vol.303
, pp. 2026-2029
-
-
Aloy, P.1
Bottcher, B.2
Ceulemans, H.3
Leutwein, C.4
Mellwig, C.5
Fischer, S.6
-
36
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin A.C., Aloy P., Grandi P., Krause R., Boesche M., and Marzioch M. Proteome survey reveals modularity of the yeast cell machinery Nature 440 2006 631 636
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
Marzioch, M.6
-
37
-
-
34447503697
-
Conformational entropy in molecular recognition by proteins
-
Frederick K.K., Marlow M.S., Valentine K.G., and Wand A.J. Conformational entropy in molecular recognition by proteins Nature 448 2007 325 329
-
(2007)
Nature
, vol.448
, pp. 325-329
-
-
Frederick, K.K.1
Marlow, M.S.2
Valentine, K.G.3
Wand, A.J.4
-
38
-
-
0030707656
-
Structural plasticity in a remodeled protein-protein interface
-
Atwell S., Ultsch M., De Vos A.M., and Wells J.A. Structural plasticity in a remodeled protein-protein interface Science 278 1997 1125 1128
-
(1997)
Science
, vol.278
, pp. 1125-1128
-
-
Atwell, S.1
Ultsch, M.2
De Vos, A.M.3
Wells, J.A.4
-
39
-
-
69449100706
-
Neutral evolution on mammalian protein surfaces
-
Conant G.C. Neutral evolution on mammalian protein surfaces Trends Genet. 25 2009 377 381
-
(2009)
Trends Genet.
, vol.25
, pp. 377-381
-
-
Conant, G.C.1
-
40
-
-
70349832423
-
Following evolutionary paths to protein-protein interactions with high affinity and selectivity
-
Levin K.B., Dym O., Albeck S., Magdassi S., Keeble A.H., Kleanthous C., and Tawfik D.S. Following evolutionary paths to protein-protein interactions with high affinity and selectivity Nat. Struct. Mol. Biol. 16 2009 1049 1055
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 1049-1055
-
-
Levin, K.B.1
Dym, O.2
Albeck, S.3
Magdassi, S.4
Keeble, A.H.5
Kleanthous, C.6
Tawfik, D.S.7
-
41
-
-
33845875196
-
Relating three-dimensional structures to protein networks provides evolutionary insights
-
Kim P.M., Lu L.J., Xia Y., and Gerstein M.B. Relating three-dimensional structures to protein networks provides evolutionary insights Science 314 2006 1938 1941
-
(2006)
Science
, vol.314
, pp. 1938-1941
-
-
Kim, P.M.1
Lu, L.J.2
Xia, Y.3
Gerstein, M.B.4
-
42
-
-
0025104478
-
Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
-
Overington J., Johnson M.S., Sali A., and Blundell T.L. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction Proc. R. Soc. Lond. B. Biol. Sci. 241 1990 132 145
-
(1990)
Proc. R. Soc. Lond. B. Biol. Sci.
, vol.241
, pp. 132-145
-
-
Overington, J.1
Johnson, M.S.2
Sali, A.3
Blundell, T.L.4
-
43
-
-
0026610767
-
Assessment of protein models with 3-dimensional profiles
-
Luthy R., Bowie J.U., and Eisenberg D. Assessment of protein models with 3-dimensional profiles Nature 356 1992 83 85
-
(1992)
Nature
, vol.356
, pp. 83-85
-
-
Luthy, R.1
Bowie, J.U.2
Eisenberg, D.3
-
44
-
-
55449117336
-
Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures
-
Gong S., and Blundell T.L. Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures PLoS Comput. Biol. 4 2008 e1000179
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. 1000179
-
-
Gong, S.1
Blundell, T.L.2
-
45
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel E., and Henrick K. Inference of macromolecular assemblies from crystalline state J. Mol. Biol. 372 2007 774 797
-
(2007)
J. Mol. Biol.
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
46
-
-
0032169688
-
PQS: A protein quaternary structure file server
-
Henrick K., and Thornton J.M. PQS: a protein quaternary structure file server Trends Biochem. Sci. 23 1998 358 361
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 358-361
-
-
Henrick, K.1
Thornton, J.M.2
-
47
-
-
47049125458
-
Statistical analysis of interface similarity in crystals of homologous proteins
-
Xu Q., Canutescu A.A., Wang G., Shapovalov M., Obradovic Z., and Dunbrack R.L. Jr Statistical analysis of interface similarity in crystals of homologous proteins J. Mol. Biol. 381 2008 487 507
-
(2008)
J. Mol. Biol.
, vol.381
, pp. 487-507
-
-
Xu, Q.1
Canutescu, A.A.2
Wang, G.3
Shapovalov, M.4
Obradovic, Z.5
Dunbrack, Jr.R.L.6
-
48
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins J. Mol. Biol. 48 1970 443 453
-
(1970)
J. Mol. Biol.
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
49
-
-
0041312697
-
Diversity of protein-protein interactions
-
Nooren I.M., and Thornton J.M. Diversity of protein-protein interactions EMBO J. 22 2003 3486 3492
-
(2003)
EMBO J.
, vol.22
, pp. 3486-3492
-
-
Nooren, I.M.1
Thornton, J.M.2
-
50
-
-
0033614004
-
Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
-
Word J.M., Lovell S.C., Richardson J.S., and Richardson D.C. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation J. Mol. Biol. 285 1999 1735 1747
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
51
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee B., and Richards F.M. The interpretation of protein structures: estimation of static accessibility J. Mol. Biol. 55 1971 379 400
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
52
-
-
0034487752
-
Exploring steric constraints on protein mutations using MAGE/PROBE
-
Word J.M., Bateman R.C., Presley B.K., Lovell S.C., and Richardson D.C. Exploring steric constraints on protein mutations using MAGE/PROBE Protein Sci. 9 2000 2251 2259
-
(2000)
Protein Sci.
, vol.9
, pp. 2251-2259
-
-
Word, J.M.1
Bateman, R.C.2
Presley, B.K.3
Lovell, S.C.4
Richardson, D.C.5
-
53
-
-
65649108490
-
Pathogenic or not? and if so, then how? Studying the effects of missense mutations using bioinformatics methods
-
Thusberg J., and Vihinen M. Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods Hum. Mutat. 30 2009 703 714
-
(2009)
Hum. Mutat.
, vol.30
, pp. 703-714
-
-
Thusberg, J.1
Vihinen, M.2
-
54
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
|