-
1
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
-
(2002)
Nature
, vol.415
, pp. 141-147
-
-
Gavin, A.C.1
Bosche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
-
2
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 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
-
3
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 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
-
4
-
-
0031565729
-
Analysis of protein-protein interaction sites using surface patches
-
Jones S, Thornton JM, (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
-
5
-
-
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
-
6
-
-
0037093645
-
Dissecting protein-protein recognition sites
-
Chakrabarti P, 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
-
-
0242299201
-
Dissecting subunit interfaces in homodimeric proteins
-
Bahadur RP, Chakrabarti P, Rodier F, Janin J, (2003) Dissecting subunit interfaces in homodimeric proteins. Proteins 53: 708-719.
-
(2003)
Proteins
, vol.53
, pp. 708-719
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
Janin, J.4
-
8
-
-
33748660856
-
Intramolecular surface contacts contain information about protein-protein interface regions
-
de Vries SJ, Bonvin AM, (2006) Intramolecular surface contacts contain information about protein-protein interface regions. Bioinformatics 22: 2094-2098.
-
(2006)
Bioinformatics
, vol.22
, pp. 2094-2098
-
-
de Vries, S.J.1
Bonvin, A.M.2
-
9
-
-
0033573827
-
Structural features of protein-nucleic acid recognition sites
-
Nadassy K, Wodak SJ, Janin J, (1999) Structural features of protein-nucleic acid recognition sites. Biochemistry 38: 1999-2017.
-
(1999)
Biochemistry
, vol.38
, pp. 1999-2017
-
-
Nadassy, K.1
Wodak, S.J.2
Janin, J.3
-
10
-
-
34548767667
-
Interaction-site prediction for protein complexes: a critical assessment
-
Zhou HX, Qin S, (2007) Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics 23: 2203-2209.
-
(2007)
Bioinformatics
, vol.23
, pp. 2203-2209
-
-
Zhou, H.X.1
Qin, S.2
-
11
-
-
52649130704
-
Protein-protein interaction and quaternary structure
-
Janin J, Bahadur RP, Chakrabarti P, (2008) Protein-protein interaction and quaternary structure. Q Rev Biophys 41: 133-180.
-
(2008)
Q Rev Biophys
, vol.41
, pp. 133-180
-
-
Janin, J.1
Bahadur, R.P.2
Chakrabarti, P.3
-
12
-
-
49249109524
-
How proteins get in touch: interface prediction in the study of biomolecular complexes
-
de Vries SJ, Bonvin AM, (2008) How proteins get in touch: interface prediction in the study of biomolecular complexes. Curr Protein Pept Sci 9: 394-406.
-
(2008)
Curr Protein Pept Sci
, vol.9
, pp. 394-406
-
-
de Vries, S.J.1
Bonvin, A.M.2
-
13
-
-
42449161827
-
The interface of protein-protein complexes: analysis of contacts and prediction of interactions
-
Bahadur RP, Zacharias M, (2008) The interface of protein-protein complexes: analysis of contacts and prediction of interactions. Cell Mol Life Sci 65: 1059-1072.
-
(2008)
Cell Mol Life Sci
, vol.65
, pp. 1059-1072
-
-
Bahadur, R.P.1
Zacharias, M.2
-
14
-
-
0035882570
-
Prediction of protein interaction sites from sequence profile and residue neighbor list
-
Zhou HX, Shan Y, (2001) Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 44: 336-343.
-
(2001)
Proteins
, vol.44
, pp. 336-343
-
-
Zhou, H.X.1
Shan, Y.2
-
15
-
-
0031565725
-
Prediction of protein-protein interaction sites using patch analysis
-
Jones S, Thornton JM, (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
-
16
-
-
33646122452
-
An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements
-
Hoskins J, Lovell S, Blundell TL, (2006) An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements. Protein Sci 15: 1017-1029.
-
(2006)
Protein Sci
, vol.15
, pp. 1017-1029
-
-
Hoskins, J.1
Lovell, S.2
Blundell, T.L.3
-
17
-
-
0042386609
-
The relationship between sequence and interaction divergence in proteins
-
Aloy P, Ceulemans H, Stark A, Russell RB, (2003) The relationship between sequence and interaction divergence in proteins. J Mol Biol 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
-
18
-
-
34249945479
-
Specificity in protein interactions and its relationship with sequence diversity and coevolution
-
Hakes L, Lovell SC, Oliver SG, Robertson DL, (2007) Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proc Natl Acad Sci U S A 104: 7999-8004.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 7999-8004
-
-
Hakes, L.1
Lovell, S.C.2
Oliver, S.G.3
Robertson, D.L.4
-
19
-
-
24344484686
-
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data
-
Chen H, Zhou HX, (2005) Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 61: 21-35.
-
(2005)
Proteins
, vol.61
, pp. 21-35
-
-
Chen, H.1
Zhou, H.X.2
-
20
-
-
1842526090
-
ProMate: a structure based prediction program to identify the location of protein-protein binding sites
-
Neuvirth H, Raz R, Schreiber G, (2004) ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 338: 181-199.
-
(2004)
J Mol Biol
, vol.338
, pp. 181-199
-
-
Neuvirth, H.1
Raz, R.2
Schreiber, G.3
-
22
-
-
0037229456
-
Analysing six types of protein-protein interfaces
-
Ofran Y, Rost B, (2003) Analysing six types of protein-protein interfaces. J Mol Biol 325: 377-387.
-
(2003)
J Mol Biol
, vol.325
, pp. 377-387
-
-
Ofran, Y.1
Rost, B.2
-
23
-
-
16344389701
-
Cation-pi interactions in protein-protein interfaces
-
Crowley PB, Golovin A, (2005) Cation-pi interactions in protein-protein interfaces. Proteins 59: 231-239.
-
(2005)
Proteins
, vol.59
, pp. 231-239
-
-
Crowley, P.B.1
Golovin, A.2
-
24
-
-
33947360625
-
PIER: protein interface recognition for structural proteomics
-
Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R, (2007) PIER: protein interface recognition for structural proteomics. Proteins 67: 400-417.
-
(2007)
Proteins
, vol.67
, pp. 400-417
-
-
Kufareva, I.1
Budagyan, L.2
Raush, E.3
Totrov, M.4
Abagyan, R.5
-
25
-
-
0028916599
-
A hot spot of binding energy in a hormone-receptor interface
-
Clackson T, Wells JA, (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267: 383-386.
-
(1995)
Science
, vol.267
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
26
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan A, Thorn K, (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.1
Thorn, K.2
-
27
-
-
0036469060
-
Unraveling hot spots in binding interfaces: progress and challenges
-
DeLano W, (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.1
-
28
-
-
0035896024
-
ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
-
Armon A, Graur D, Ben-Tal N, (2001) ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 307: 447-463.
-
(2001)
J Mol Biol
, vol.307
, pp. 447-463
-
-
Armon, A.1
Graur, D.2
Ben-Tal, N.3
-
29
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O, Bourne HR, Cohen FE, (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
-
30
-
-
33646182934
-
An integrated view of protein evolution
-
Pal C, Papp B, Lercher MJ, (2006) An integrated view of protein evolution. Nat Rev Genet 7: 337-348.
-
(2006)
Nat Rev Genet
, vol.7
, pp. 337-348
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
31
-
-
77958114505
-
An integrated view of molecular coevolution in protein-protein interactions
-
Lovell SC, Robertson DL, An integrated view of molecular coevolution in protein-protein interactions. Mol Biol Evol 27: 2567-2575.
-
Mol Biol Evol
, vol.27
, pp. 2567-2575
-
-
Lovell, S.C.1
Robertson, D.L.2
-
32
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Research 28: 235-242.
-
(2000)
Nucleic Acids Research
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
33
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel E, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797.
-
(2007)
J Mol Biol
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
34
-
-
0032169688
-
PQS: a protein quaternary structure file server
-
Henrick K, Thornton JM, (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
-
35
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD, (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
36
-
-
0033614004
-
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation
-
Word JM, Lovell SC, Richardson JS, Richardson DC, (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285: 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
-
37
-
-
0033613812
-
Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms
-
Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, et al. (1999) Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 285: 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
-
38
-
-
0015222647
-
The interpretation of protein structures: estimation of static accessibility
-
Lee B, Richards FM, (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55: 379-400.
-
(1971)
J Mol Biol
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
39
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman D, Argos P, (1995) Knowledge-based protein secondary structure assignment. Proteins 23: 566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
40
-
-
33751083105
-
A fast method for the determination of fractional contributions to solvation in proteins
-
Talavera D, Morreale A, Meyer T, Hospital A, Ferrer-Costa C, et al. (2006) A fast method for the determination of fractional contributions to solvation in proteins. Protein Sci 15: 2525-2533.
-
(2006)
Protein Sci
, vol.15
, pp. 2525-2533
-
-
Talavera, D.1
Morreale, A.2
Meyer, T.3
Hospital, A.4
Ferrer-Costa, C.5
-
41
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy P, Russell RB, (2002) Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci U S A 99: 5896-5901.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
42
-
-
0024290488
-
Helix Signals in Proteins
-
Presta LG, Rose GD, (1988) Helix Signals in Proteins. Science 240: 1632-1641.
-
(1988)
Science
, vol.240
, pp. 1632-1641
-
-
Presta, L.G.1
Rose, G.D.2
-
43
-
-
0024290472
-
Amino acid preferences for specific locations at the ends of alpha helices [published erratum appears in Science 1988 Dec 23;242(4886):1624]
-
Richardson JS, Richardson DC, (1988) Amino acid preferences for specific locations at the ends of alpha helices [published erratum appears in Science 1988 Dec 23;242(4886):1624]. Science 240: 1648-1652.
-
(1988)
Science
, vol.240
, pp. 1648-1652
-
-
Richardson, J.S.1
Richardson, D.C.2
-
44
-
-
0037022563
-
Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation
-
Richardson JS, Richardson DC, (2002) Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci U S A 99: 2754-2759.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 2754-2759
-
-
Richardson, J.S.1
Richardson, D.C.2
-
45
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris J, Weng Z, (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A 102: 10930-10935.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
46
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte J, Doolittle RF, (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
|