-
1
-
-
70350482286
-
Evolution of biomolecular networks - Lessons from metabolic and protein interactions
-
Yamada T, Bork P (2009) Evolution of biomolecular networks - lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol 10:791-803.
-
(2009)
Nat Rev Mol Cell Biol
, vol.10
, pp. 791-803
-
-
Yamada, T.1
Bork, P.2
-
3
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han J-DJ, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJM, Cusick ME, Roth FP, Vidal M (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430:88-93.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.-D.J.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.M.8
Cusick, M.E.9
Roth, F.P.10
Vidal, M.11
-
4
-
-
33746631391
-
Evolutionary and physiological importance of hub proteins
-
doi: 10.1371/journal.pcbi.0020088
-
Batada NN, Hurst LD, Tyers M (2006) Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2:e88. doi: 10.1371/journal.pcbi. 0020088.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Batada, N.N.1
Hurst, L.D.2
Tyers, M.3
-
5
-
-
33845875196
-
Relating three-dimensional structures to protein networks provides evolutionary insights
-
DOI 10.1126/science.1136174
-
Kim PM, Lu LJ, Xia Y, Gerstein MB (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314:1938-1941. (Pubitemid 46026118)
-
(2006)
Science
, vol.314
, Issue.5807
, pp. 1938-1941
-
-
Kim, P.M.1
Lu, L.J.2
Xia, Y.3
Gerstein, M.B.4
-
6
-
-
27144464910
-
Flexible nets
-
Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN (2005) Flexible nets. FEBS J 272:5129-5148.
-
(2005)
FEBS J
, vol.272
, pp. 5129-5148
-
-
Dunker, A.K.1
Cortese, M.S.2
Romero, P.3
Iakoucheva, L.M.4
Uversky, V.N.5
-
7
-
-
33745686603
-
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?
-
doi: 10.1186/gb-2006-7-6-r45
-
Ekman D, Light S, Bjorklund A, Elofsson A (2006) What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol 7:R45. doi: 10.1186/gb-2006-7-6-r45.
-
(2006)
Genome Biol
, vol.7
-
-
Ekman, D.1
Light, S.2
Bjorklund, A.3
Elofsson, A.4
-
8
-
-
33748074139
-
Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes
-
doi: 10.1371/journal.pcbi.0020100
-
Haynes C, Oldfield CJ, Ji F, Klitgord N, Cusick ME, Radivojac P, Uversky VN, Vidal M, Iakoucheva LM (2006) Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol 2:e100. doi: 10.1371/journal.pcbi.0020100.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Haynes, C.1
Oldfield, C.J.2
Ji, F.3
Klitgord, N.4
Cusick, M.E.5
Radivojac, P.6
Uversky, V.N.7
Vidal, M.8
Iakoucheva, L.M.9
-
9
-
-
33645214608
-
Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks
-
Patil A, Nakamura H (2006) Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks. FEBS Lett 580:2041-2045.
-
(2006)
FEBS Lett
, vol.580
, pp. 2041-2045
-
-
Patil, A.1
Nakamura, H.2
-
10
-
-
34547125807
-
The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks
-
DOI 10.2142/biophysics.3.27
-
Patil A, Nakamura H (2007) The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks. Biophysics 3:27-35. (Pubitemid 47104969)
-
(2007)
Biophysics
, vol.3
, pp. 27-35
-
-
Patil, A.1
Nakamura, H.2
-
11
-
-
59849106371
-
Protein promiscuity and its implications for biotechnology
-
Nobeli I, Favia AD, Thornton JM (2009) Protein promiscuity and its implications for biotechnology. Nat Biotechnol 27:157-167.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 157-167
-
-
Nobeli, I.1
Favia, A.D.2
Thornton, J.M.3
-
12
-
-
70449769325
-
Protein-protein interaction networks: How can a hub protein bind so many different partners?
-
Tsai CJ, Ma B, Nussinov R (2009) Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci 34:594-600.
-
(2009)
Trends Biochem Sci
, vol.34
, pp. 594-600
-
-
Tsai, C.J.1
Ma, B.2
Nussinov, R.3
-
13
-
-
1842861592
-
Structure, function and evolution of multidomain proteins
-
DOI 10.1016/j.sbi.2004.03.011, PII S0959440X04000454
-
Vogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA (2004) Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol 14:208-216. (Pubitemid 38490788)
-
(2004)
Current Opinion in Structural Biology
, vol.14
, Issue.2
, pp. 208-216
-
-
Vogel, C.1
Bashton, M.2
Kerrison, N.D.3
Chothia, C.4
Teichmann, S.A.5
-
14
-
-
67650497792
-
Nature of the protein universe
-
Levitt M (2009) Nature of the protein universe. Proc Natl Acad Sci USA 106:11079-11084.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 11079-11084
-
-
Levitt, M.1
-
15
-
-
34548383489
-
Design of multispecificity in protein interfaces
-
doi: 10.1371/journal.pcbi.0030164
-
Humphris EL, Kortemme T (2007) Design of multispecificity in protein interfaces. PLoS Comput Biol 3: e164. doi: 10.1371/journal.pcbi.0030164.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Humphris, E.L.1
Kortemme, T.2
-
16
-
-
59849125136
-
Dynamic modularity in protein interaction networks predicts breast cancer outcome
-
Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 27:199-204.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 199-204
-
-
Taylor, I.W.1
Linding, R.2
Warde-Farley, D.3
Liu, Y.4
Pesquita, C.5
Faria, D.6
Bull, S.7
Pawson, T.8
Morris, Q.9
Wrana, J.L.10
-
17
-
-
38549146894
-
The Pfam protein families database
-
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz H-R, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL, Bateman A (2008) The Pfam protein families database. Nucl Acids Res 36:D281-D288.
-
(2008)
Nucl Acids Res
, vol.36
-
-
Finn, R.D.1
Tate, J.2
Mistry, J.3
Coggill, P.C.4
Sammut, S.J.5
Hotz, H.-R.6
Ceric, G.7
Forslund, K.8
Eddy, S.R.9
Sonnhammer, E.L.L.10
Bateman, A.11
-
18
-
-
65449152586
-
Identifying hubs in protein interaction networks
-
doi: 10.1371/journal.pone.0005344
-
Vallabhajosyula RR, Chakravarti D, Lutfeali S, Ray A, Raval A (2009) Identifying hubs in protein interaction networks. PLoS ONE 4:e5344. doi: 10.1371/journal.pone.0005344.
-
(2009)
PLoS ONE
, vol.4
-
-
Vallabhajosyula, R.R.1
Chakravarti, D.2
Lutfeali, S.3
Ray, A.4
Raval, A.5
-
19
-
-
43149092276
-
Principles of protein-protein interactions: What are the preferred ways for proteins to interact?
-
Keskin O, Gursoy A, Ma B, Nussinov R (2008) Principles of protein-protein interactions: what are the preferred ways for proteins to interact? Chem Rev 108: 1225-1244.
-
(2008)
Chem Rev
, vol.108
, pp. 1225-1244
-
-
Keskin, O.1
Gursoy, A.2
Ma, B.3
Nussinov, R.4
-
20
-
-
41149119083
-
The role of disorder in interaction networks: A structural analysis
-
doi: 10.1038/msb.2008.16
-
Kim PM, Sboner A, Xia Y, Gerstein M (2008) The role of disorder in interaction networks: a structural analysis. Mol Syst Biol 4:179. doi: 10.1038/msb.2008.16.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 179
-
-
Kim, P.M.1
Sboner, A.2
Xia, Y.3
Gerstein, M.4
-
21
-
-
0032836911
-
Human replication protein A: Global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible C-terminal linker
-
Jacobs DM, Lipton AS, Isern NG, Daughdrill GW, Lowry DF, Gomes X, Wold MS (1999) Human replication protein A: global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible C-terminal linker. J Biomol NMR 14:321-331.
-
(1999)
J Biomol NMR
, vol.14
, pp. 321-331
-
-
Jacobs, D.M.1
Lipton, A.S.2
Isern, N.G.3
Daughdrill, G.W.4
Lowry, D.F.5
Gomes, X.6
Wold, M.S.7
-
22
-
-
0037032835
-
The protein kinase complement of the human genome
-
Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S (2002) The protein kinase complement of the human genome. Science 298:1912-1934.
-
(2002)
Science
, vol.298
, pp. 1912-1934
-
-
Manning, G.1
Whyte, D.B.2
Martinez, R.3
Hunter, T.4
Sudarsanam, S.5
-
23
-
-
34547743903
-
Reuse of structural domain-domain interactions in protein networks
-
doi: 10.1186/1471-2105-8-259
-
Schuster-Bockler B, Bateman A (2007) Reuse of structural domain-domain interactions in protein networks. BMC Bioinformatics 8:259. doi: 10.1186/1471-2105-8-259.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 259
-
-
Schuster-Bockler, B.1
Bateman, A.2
-
24
-
-
33847768609
-
Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions
-
Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Uversky VN, Obradovic Z (2007) Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res 6:1882-1898.
-
(2007)
J Proteome Res
, vol.6
, pp. 1882-1898
-
-
Xie, H.1
Vucetic, S.2
Iakoucheva, L.M.3
Oldfield, C.J.4
Dunker, A.K.5
Uversky, V.N.6
Obradovic, Z.7
-
25
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5:101-113.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
26
-
-
34247622363
-
The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics
-
doi: 10.1371/journal.pcbi.0030059
-
Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 3:e59. doi: 10.1371/journal.pcbi.0030059.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Yu, H.1
Kim, P.M.2
Sprecher, E.3
Trifonov, V.4
Gerstein, M.5
-
27
-
-
33846047770
-
IntAct - Open source resource for molecular interaction data
-
Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H (2007) IntAct - open source resource for molecular interaction data. Nucl Acids Res 35:D561-D565.
-
(2007)
Nucl Acids Res
, vol.35
-
-
Kerrien, S.1
Alam-Faruque, Y.2
Aranda, B.3
Bancarz, I.4
Bridge, A.5
Derow, C.6
Dimmer, E.7
Feuermann, M.8
Friedrichsen, A.9
Huntley, R.10
Kohler, C.11
Khadake, J.12
Leroy, C.13
Liban, A.14
Lieftink, C.15
Montecchi-Palazzi, L.16
Orchard, S.17
Risse, J.18
Robbe, K.19
Roechert, B.20
Thorneycroft, D.21
Zhang, Y.22
Apweiler, R.23
Hermjakob, H.24
more..
-
28
-
-
38549173606
-
The BioGRID Interaction Database: 2008 Update
-
Breitkreutz B-J, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bahler J, Wood V, Dolinski K, Tyers M (2008) The BioGRID Interaction Database: 2008 update. Nucl Acids Res 36: D637-D640.
-
(2008)
Nucl Acids Res
, vol.36
-
-
Breitkreutz, B.-J.1
Stark, C.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Livstone, M.6
Oughtred, R.7
Lackner, D.H.8
Bahler, J.9
Wood, V.10
Dolinski, K.11
Tyers, M.12
-
29
-
-
58149193222
-
Human Protein Reference Database - 2009 Update
-
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A (2009) Human Protein Reference Database - 2009 update. Nucl Acids Res 37:D767-D772.
-
(2009)
Nucl Acids Res
, vol.37
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
Keerthikumar, S.4
Kumar, S.5
Mathivanan, S.6
Telikicherla, D.7
Raju, R.8
Shafreen, B.9
Venugopal, A.10
Balakrishnan, L.11
Marimuthu, A.12
Banerjee, S.13
Somanathan, D.S.14
Sebastian, A.15
Rani, S.16
Ray, S.17
Harrys Kishore, C.J.18
Kanth, S.19
Ahmed, M.20
Kashyap, M.K.21
Mohmood, R.22
Ramachandra, Y.L.23
Krishna, V.24
Rahiman, B.A.25
Mohan, S.26
Ranganathan, P.27
Ramabadran, S.28
Chaerkady, R.29
Pandey, A.30
more..
-
30
-
-
0036789265
-
Analyzing yeast protein-protein interaction data obtained from different sources
-
Bader GD, Hogue CW (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 20:991-997.
-
(2002)
Nat Biotechnol
, vol.20
, pp. 991-997
-
-
Bader, G.D.1
Hogue, C.W.2
-
31
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399-403. (Pubitemid 34563526)
-
(2002)
Nature
, vol.417
, Issue.6887
, pp. 399-403
-
-
Von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
32
-
-
24044434446
-
Filtering high-throughput protein-protein interaction data using a combination of genomic features
-
doi: 10.1186/1471-2105-6-100
-
Patil A, Nakamura H (2005) Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics 6:100. doi: 10.1186/1471-2105-6-100.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 100
-
-
Patil, A.1
Nakamura, H.2
-
33
-
-
25444433570
-
HINT: A database of annotated protein-protein interactions and their homologs
-
Patil A, Nakamura H (2005) HINT: a database of annotated protein-protein interactions and their homologs. Biophysics 1:21-24.
-
(2005)
Biophysics
, vol.1
, pp. 21-24
-
-
Patil, A.1
Nakamura, H.2
-
34
-
-
44349192171
-
Prediction of disordered regions in proteins based on the meta approach
-
DOI 10.1093/bioinformatics/btn195
-
Ishida T, Kinoshita K (2008) Prediction of disordered regions in proteins based on the meta approach. Bioinformatics 24:1344-1348. (Pubitemid 351737139)
-
(2008)
Bioinformatics
, vol.24
, Issue.11
, pp. 1344-1348
-
-
Ishida, T.1
Kinoshita, K.2
-
35
-
-
38349164409
-
Computing topological parameters of biological networks
-
Assenov Y, Ramirez F, Schelhorn S-E, Lengauer T, Albrecht M (2008) Computing topological parameters of biological networks. Bioinformatics 24:282-284.
-
(2008)
Bioinformatics
, vol.24
, pp. 282-284
-
-
Assenov, Y.1
Ramirez, F.2
Schelhorn, S.-E.3
Lengauer, T.4
Albrecht, M.5
-
36
-
-
0242490780
-
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
-
DOI 10.1101/gr.1239303
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-2504. (Pubitemid 37428274)
-
(2003)
Genome Research
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
|