-
1
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Poc Natl Acad Sci. 2001; 98(8):4569-4574. doi: 10.1073/pnas. 061034498
-
(2001)
Poc Natl Acad Sci.
, vol.98
, Issue.8
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
2
-
-
0037050004
-
Systematic identification of protein complexes in saccharomyces cerevisiae by mass spectrometry
-
PMID: 11805837
-
Ho Y, et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002; 415(6868):180-183. doi: 10.1038/415180a PMID: 11805837
-
(2002)
Nature
, vol.415
, Issue.6868
, pp. 180-183
-
-
Ho, Y.1
-
3
-
-
58149242456
-
An experimentally derived confidence score for binary protein-protein interactions
-
PMID: 19060903
-
Braun P, et al. An experimentally derived confidence score for binary protein-protein interactions. Nature methods. 2008; 6(1):91-97. doi: 10.1038/nmeth.1281 PMID: 19060903
-
(2008)
Nature Methods
, vol.6
, Issue.1
, pp. 91-97
-
-
Braun, P.1
-
4
-
-
41149141724
-
Predicting biological networks from genomic data
-
PMID: 18294967
-
Harrington ED, Jensen LJ, Bork P. Predicting biological networks from genomic data. FEBS letters. 2008; 582(8):1251-1258. doi: 10.1016/j.febslet.2008.02.033 PMID: 18294967
-
(2008)
FEBS Letters
, vol.582
, Issue.8
, pp. 1251-1258
-
-
Harrington, E.D.1
Jensen, L.J.2
Bork, P.3
-
5
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
PMID: 9787636
-
Dandekar T, Snel B, Huynen M, Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends in biochemical sciences. 1998; 23(9):324-328. doi: 10.1016/S0968-0004(98) 01274-2 PMID: 9787636
-
(1998)
Trends in Biochemical Sciences
, vol.23
, Issue.9
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
6
-
-
0034084865
-
Who's your neighbor? New computational approaches for functional genomics
-
PMID: 10835597
-
Galperin MY, Koonin EV. Who's your neighbor? New computational approaches for functional genomics. Nature biotechnology. 2000; 18(6):609-613. doi: 10.1038/76443 PMID: 10835597
-
(2000)
Nature Biotechnology
, vol.18
, Issue.6
, pp. 609-613
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
7
-
-
0041845736
-
Predicting functional linkages from gene fusions with confidence
-
PMID: 15130848
-
Marcotte CJV, Marcotte EM. Predicting functional linkages from gene fusions with confidence. Applied bioinformatics. 2002; 1(2):93-100. PMID: 15130848
-
(2002)
Applied Bioinformatics
, vol.1
, Issue.2
, pp. 93-100
-
-
Marcotte, C.J.V.1
Marcotte, E.M.2
-
8
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Poc Natl Acad Sci. 1999; 96(8):4285-4288. doi: 10.1073/pnas.96.8.4285
-
(1999)
Poc Natl Acad Sci.
, vol.96
, Issue.8
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
9
-
-
0036601150
-
Computational methods for the prediction of protein interactions
-
PMID: 12127457
-
Valencia A, Pazos F. Computational methods for the prediction of protein interactions. Current Opinion in Structural Biology. 2002; 12(3):368-373. Available from: http://www.sciencedirect.com/science/article/pii/S0959440X02003330. doi: 10.1016/S0959-440X(02)00333-0 PMID: 12127457
-
(2002)
Current Opinion in Structural Biology
, vol.12
, Issue.3
, pp. 368-373
-
-
Valencia, A.1
Pazos, F.2
-
10
-
-
0036568319
-
In silico two-hybrid system for the selection of physically interacting protein pairs
-
Pazos F, Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins: Structure, Function, and Bioinformatics. 2002; 47(2):219-227. doi: 10.1002/prot.10074
-
(2002)
Proteins: Structure, Function, and Bioinformatics
, vol.47
, Issue.2
, pp. 219-227
-
-
Pazos, F.1
Valencia, A.2
-
11
-
-
36949019322
-
Detecting coevolution in and among protein domains
-
11. PMID: 17983264
-
Yeang CH, Haussler D. Detecting Coevolution in and among Protein Domains. PLoS Comput Biol. 2007 11; 3(11):e211. doi: 10.1371/journal.pcbi.0030211 PMID: 17983264
-
(2007)
PLoS Comput Biol.
, vol.3
, Issue.11
, pp. e211
-
-
Yeang, C.H.1
Haussler, D.2
-
12
-
-
38949168935
-
High-confidence prediction of global interactomes based on genomewide coevolutionary networks
-
Juan D, Pazos F, Valencia A. High-confidence prediction of global interactomes based on genomewide coevolutionary networks. Poc Natl Acad Sci. 2008; 105(3):934-939. doi: 10.1073/pnas. 0709671105
-
(2008)
Poc Natl Acad Sci.
, vol.105
, Issue.3
, pp. 934-939
-
-
Juan, D.1
Pazos, F.2
Valencia, A.3
-
14
-
-
58549114185
-
Identification of direct residue contacts in protein-protein interaction by message passing
-
Weigt M, White RA, Szurmant H, Hoch JA, Hwa T. Identification of direct residue contacts in protein-protein interaction by message passing. Poc Natl Acad Sci. 2009; 106(1):67-72. doi: 10.1073/pnas. 0805923106
-
(2009)
Poc Natl Acad Sci.
, vol.106
, Issue.1
, pp. 67-72
-
-
Weigt, M.1
White, R.A.2
Szurmant, H.3
Hoch, J.A.4
Hwa, T.5
-
15
-
-
83755178457
-
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
-
Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, et al. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Poc Natl Acad Sci. 2011; 108 (49):E1293-E1301. doi: 10.1073/pnas.1111471108
-
(2011)
Poc Natl Acad Sci.
, vol.108
, Issue.49
, pp. E1293-E1301
-
-
Morcos, F.1
Pagnani, A.2
Lunt, B.3
Bertolino, A.4
Marks, D.S.5
Sander, C.6
-
16
-
-
84891782659
-
Pfam: The protein families database
-
PMID: 24288371
-
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Research. 2014; 42(D1):D222-D230. doi: 10.1093/nar/gkt1223 PMID: 24288371
-
(2014)
Nucleic Acids Research
, vol.42
, Issue.D1
, pp. D222-D230
-
-
Finn, R.D.1
Bateman, A.2
Clements, J.3
Coggill, P.4
Eberhardt, R.Y.5
Eddy, S.R.6
-
17
-
-
84872521100
-
Improved contact prediction in proteins: Using pseudolikelihoods to infer potts models
-
Ekeberg M, Lövkvist C, Lan Y, Weigt M, Aurell E. Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models. Physical Review E. 2013; 87(1):012707. doi: 10.1103/PhysRevE. 87.012707
-
(2013)
Physical Review E
, vol.87
, Issue.1
, pp. 012707
-
-
Ekeberg, M.1
Lövkvist, C.2
Lan, Y.3
Weigt, M.4
Aurell, E.5
-
18
-
-
84899707813
-
Fast and accurate multivariate Gaussian modeling of protein families: Predicting residue contacts and protein-interaction partners
-
PMID: 24663061
-
Baldassi C, Zamparo M, Feinauer C, Procaccini A, Zecchina R, Weigt M, et al. Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners. PLoS ONE. 2014; 9(3):e92721. doi: 10.1371/journal.pone.0092721 PMID: 24663061
-
(2014)
PLoS One
, vol.9
, Issue.3
, pp. e92721
-
-
Baldassi, C.1
Zamparo, M.2
Feinauer, C.3
Procaccini, A.4
Zecchina, R.5
Weigt, M.6
-
19
-
-
79952488320
-
Learning generative models for protein fold families
-
Balakrishnan S, Kamisetty H, Carbonell JG, Lee SI, Langmead CJ. Learning generative models for protein fold families. Proteins: Struct, Funct, Bioinf. 2011; 79:1061. doi: 10.1002/prot.22934
-
(2011)
Proteins: Struct, Funct, Bioinf
, vol.79
, pp. 1061
-
-
Balakrishnan, S.1
Kamisetty, H.2
Carbonell, J.G.3
Lee, S.I.4
Langmead, C.J.5
-
20
-
-
84899847547
-
Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information
-
PMID: 24842992
-
Ovchinnikov S, Kamisetty H, Baker D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. eLife. 2014; 3. doi: 10.7554/eLife.02030 PMID: 24842992
-
(2014)
ELife
, vol.3
-
-
Ovchinnikov, S.1
Kamisetty, H.2
Baker, D.3
-
21
-
-
84994885238
-
Sequence coevolution gives 3D contacts and structures of protein complexes
-
PMID: 25255213
-
Hopf TA, Schärfe CPI, Rodrigues JPGLM, Green AG, Kohlbacher O, Sander C, et al. Sequence coevolution gives 3D contacts and structures of protein complexes. eLife. 2014; 3. doi: 10.7554/eLife. 03430 PMID: 25255213
-
(2014)
ELife
, vol.3
-
-
Hopf, T.A.1
Schärfe, C.P.I.2
Rodrigues, J.P.G.L.M.3
Green, A.G.4
Kohlbacher, O.5
Sander, C.6
-
22
-
-
76049105937
-
High-resolution protein complexes from integrating genomic information with molecular simulation
-
Schug A, Weigt M, Onuchic JN, Hwa T, Szurmant H. High-resolution protein complexes from integrating genomic information with molecular simulation. Poc Natl Acad Sci. 2009; 106(52):22124-22129. doi: 10.1073/pnas.0912100106
-
(2009)
Poc Natl Acad Sci.
, vol.106
, Issue.52
, pp. 22124-22129
-
-
Schug, A.1
Weigt, M.2
Onuchic, J.N.3
Hwa, T.4
Szurmant, H.5
-
23
-
-
84863006375
-
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis
-
Dago AE, Schug A, Procaccini A, Hoch JA, Weigt M, Szurmant H. Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. Poc Natl Acad Sci. 2012; 109(26):E1733-E1742. doi: 10.1073/pnas.1201301109
-
(2012)
Poc Natl Acad Sci.
, vol.109
, Issue.26
, pp. E1733-E1742
-
-
Dago, A.E.1
Schug, A.2
Procaccini, A.3
Hoch, J.A.4
Weigt, M.5
Szurmant, H.6
-
24
-
-
39149114704
-
Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
-
PMID: 18277381
-
Burger L, Van Nimwegen E. Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Molecular Systems Biology. 2008; 4(165):165. doi: 10.1038/msb4100203 PMID: 18277381
-
(2008)
Molecular Systems Biology
, vol.4
, Issue.165
, pp. 165
-
-
Burger, L.1
Van Nimwegen, E.2
-
25
-
-
79955792165
-
Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: Orphans and crosstalks
-
PMID: 21573011
-
Procaccini A, Lunt B, Szurmant H, Hwa T, Weigt M. Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks. PloS one. 2011; 6(5):e19729. doi: 10.1371/journal.pone.0019729 PMID: 21573011
-
(2011)
PloS One
, vol.6
, Issue.5
, pp. e19729
-
-
Procaccini, A.1
Lunt, B.2
Szurmant, H.3
Hwa, T.4
Weigt, M.5
-
26
-
-
84893476565
-
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information
-
Cheng RR, Morcos F, Levine H, Onuchic JN. Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Poc Natl Acad Sci. 2014; 111(5):E563-E571. doi: 10.1073/pnas.1323734111
-
(2014)
Poc Natl Acad Sci.
, vol.111
, Issue.5
, pp. E563-E571
-
-
Cheng, R.R.1
Morcos, F.2
Levine, H.3
Onuchic, J.N.4
-
27
-
-
0033578351
-
The crystal structure of anthranilate synthase from sulfolobus solfataricus: Functional implications
-
Knöchel T, Ivens A, Hester G, Gonzalez A, Bauerle R, Wilmanns M, et al. The crystal structure of anthranilate synthase from Sulfolobus solfataricus: Functional implications. Proceedings of the National Academy of Sciences. 1999; 96(17):9479-9484. Available from: http://www.pnas.org/content/96/17/9479.abstract. doi: 10.1073/pnas.96.17.9479
-
(1999)
Proceedings of the National Academy of Sciences
, vol.96
, Issue.17
, pp. 9479-9484
-
-
Knöchel, T.1
Ivens, A.2
Hester, G.3
Gonzalez, A.4
Bauerle, R.5
Wilmanns, M.6
-
28
-
-
0037155812
-
Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase
-
PMID: 11756456
-
Weyand M, Schlichting I, Marabotti A, Mozzarelli A. Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase. Journal of Biological Chemistry. 2002; 277(12):10647-10652. doi: 10.1074/jbc.M111285200 PMID: 11756456
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.12
, pp. 10647-10652
-
-
Weyand, M.1
Schlichting, I.2
Marabotti, A.3
Mozzarelli, A.4
-
29
-
-
84946069451
-
UniProt: A hub for protein information
-
PMID: 25348405
-
Consortium TU. UniProt: a hub for protein information. Nucleic Acids Research. 2015; 43(D1):D204-D212. Available from: http://nar.oxfordjournals.org/content/43/D1/D204.abstract. doi: 10.1093/nar/gku989 PMID: 25348405
-
(2015)
Nucleic Acids Research
, vol.43
, Issue.D1
, pp. D204-D212
-
-
Consortium, T.U.1
-
30
-
-
84908313189
-
Improving contact prediction along three dimensions
-
10. PMID: 25299132
-
Feinauer C, Skwark MJ, Pagnani A, Aurell E. Improving Contact Prediction along Three Dimensions. PLoS Comput Biol. 2014 10; 10:e1003847. doi: 10.1371/journal.pcbi.1003847 PMID: 25299132
-
(2014)
PLoS Comput Biol.
, vol.10
, pp. e1003847
-
-
Feinauer, C.1
Skwark, M.J.2
Pagnani, A.3
Aurell, E.4
-
31
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast fourier transform
-
PMID: 12136088
-
Katoh K, Misawa K, Kuma Ki, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research. 2002; 30(14):3059-3066. doi: 10.1093/nar/gkf436 PMID: 12136088
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.14
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Ki, K.3
Miyata, T.4
-
32
-
-
79959931985
-
HMMER web server: Interactive sequence similarity searching
-
p. gkr367
-
Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic acids research. 2011;p. gkr367. doi: 10.1093/nar/gkr367
-
(2011)
Nucleic Acids Research
-
-
Finn, R.D.1
Clements, J.2
Eddy, S.R.3
-
33
-
-
79959828326
-
Testing the ortholog conjecture with comparative functional genomic data from mammals
-
June. PMID: 21695233
-
Nehrt NL, Clark WT, Radivojac P, Hahn MW. Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS computational biology. 2011 June; 7(6):e1002073. Available from: http://europepmc.org/articles/PMC3111532. doi: 10.1371/journal.pcbi.1002073 PMID: 21695233
-
(2011)
PLoS Computational Biology
, vol.7
, Issue.6
, pp. e1002073
-
-
Nehrt, N.L.1
Clark, W.T.2
Radivojac, P.3
Hahn, M.W.4
-
34
-
-
84863639111
-
Resolving the ortholog conjecture: Orthologs tend to Be weakly, but significantly, more similar in function than paralogs
-
05. PMID: 22615551
-
Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C. Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs. PLoS Comput Biol. 2012 05; 8(5):e1002514. doi: 10.1371/journal.pcbi.1002514 PMID: 22615551
-
(2012)
PLoS Comput Biol.
, vol.8
, Issue.5
, pp. e1002514
-
-
Altenhoff, A.M.1
Studer, R.A.2
Robinson-Rechavi, M.3
Dessimoz, C.4
-
35
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N. The use of gene clusters to infer functional coupling. Proceedings of the National Academy of Sciences. 1999; 96(6):2896-2901. Available from: http://www.pnas.org/content/96/6/2896.abstract. doi: 10.1073/pnas.96.6.2896
-
(1999)
Proceedings of the National Academy of Sciences
, vol.96
, Issue.6
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
36
-
-
0034306448
-
Gene context conservation of a higher order than operons
-
PMID: 11050428
-
Lathe WC, Snel B, Bork P. Gene context conservation of a higher order than operons. Trends in biochemical sciences. 2000; 25(10):474-479. doi: 10.1016/S0968-0004(00)01663-7 PMID: 11050428
-
(2000)
Trends in Biochemical Sciences
, vol.25
, Issue.10
, pp. 474-479
-
-
Lathe, W.C.1
Snel, B.2
Bork, P.3
-
37
-
-
9144230986
-
Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes
-
PMID: 15260894
-
Rogozin IB, Makarova KS, Wolf YI, Koonin EV. Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Briefings in Bioinformatics. 2004; 5(2):131-149. Available from: http://bib.oxfordjournals.org/content/5/2/131.abstract. doi: 10.1093/bib/5.2.131 PMID: 15260894
-
(2004)
Briefings in Bioinformatics
, vol.5
, Issue.2
, pp. 131-149
-
-
Rogozin, I.B.1
Makarova, K.S.2
Wolf, Y.I.3
Koonin, E.V.4
-
38
-
-
0021603710
-
Structure of bovine pancreatic trypsin inhibitor: Results of joint neutron and X-ray refinement of crystal form II
-
PMID: 6210373
-
Wlodawer A, Walter J, Huber R, Sjölin L. Structure of bovine pancreatic trypsin inhibitor: Results of joint neutron and X-ray refinement of crystal form II. Journal of Molecular Biology. 1984; 180(2):301-329. doi: 10.1016/S0022-2836(84)80006-6 PMID: 6210373
-
(1984)
Journal of Molecular Biology
, vol.180
, Issue.2
, pp. 301-329
-
-
Wlodawer, A.1
Walter, J.2
Huber, R.3
Sjölin, L.4
-
39
-
-
34547696927
-
Structural basis for aminoglycoside inhibition of bacterial ribosome recycling
-
Borovinskaya MA, et al. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nature Struct Mol Biol. 2007; 14(8):727-732. doi: 10.1038/nsmb1271
-
(2007)
Nature Struct Mol Biol.
, vol.14
, Issue.8
, pp. 727-732
-
-
Borovinskaya, M.A.1
-
40
-
-
0026584311
-
Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: Indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 Å resolution
-
PMID: 1738159
-
Wilmanns M, Priestle JP, Niermann T, Jansonius JN. Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: Indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 Å resolution. Journal of Molecular Biology. 1992; 223(2):477-507. Available from: http://www.sciencedirect.com/science/article/pii/0022283692906657. doi: 10.1016/0022-2836(92) 90665-7 PMID: 1738159
-
(1992)
Journal of Molecular Biology
, vol.223
, Issue.2
, pp. 477-507
-
-
Wilmanns, M.1
Priestle, J.P.2
Niermann, T.3
Jansonius, J.N.4
|