-
1
-
-
84986522918
-
ICM-a method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
-
Abagyan R, Totrov M, Kuznetsov D (1994) ICM-a method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15:488-506
-
(1994)
J Comput Chem
, vol.15
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kuznetsov, D.3
-
2
-
-
33646568805
-
Gene prioritization through genomic data fusion
-
Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y (2006) Gene prioritization through genomic data fusion. Nat Biotechnol 24:537-544
-
(2006)
Nat Biotechnol
, vol.24
, pp. 537-544
-
-
Aerts, S.1
Lambrechts, D.2
Maity, S.3
Van Loo, P.4
Coessens, B.5
De Smet, F.6
Tranchevent, L.C.7
De Moor, B.8
Marynen, P.9
Hassan, B.10
Carmeliet, P.11
Moreau, Y.12
-
3
-
-
27944493925
-
Scale-free networks in cell biology
-
Albert R (2005) Scale-free networks in cell biology. J Cell Sci 118:4947-4957
-
(2005)
J Cell Sci
, vol.118
, pp. 4947-4957
-
-
Albert, R.1
-
4
-
-
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
-
5
-
-
5044235050
-
Ten thousand interactions for the molecular biologist
-
Aloy P, Russell RB (2004) Ten thousand interactions for the molecular biologist. Nat Biotechnol 22:1317-1321
-
(2004)
Nat Biotechnol
, vol.22
, pp. 1317-1321
-
-
Aloy, P.1
Russell, R.B.2
-
6
-
-
33644550021
-
Structural systems biology: Modelling protein interactions
-
Aloy P, Russell RB (2006) Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 7:188-197
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, pp. 188-197
-
-
Aloy, P.1
Russell, R.B.2
-
7
-
-
0346494941
-
SCOP database in 2004: Refinements integrate structure and sequence family data
-
Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 32:D226-D229
-
(2004)
Nucleic Acids Res
, vol.32
, pp. D226-D229
-
-
Andreeva, A.1
Howorth, D.2
Brenner, S.E.3
Hubbard, T.J.4
Chothia, C.5
Murzin, A.G.6
-
8
-
-
0035816218
-
Domain combinations in archaeal, eubacterial and eukaryotic proteomes
-
Apic G, Gough J, Teichmann SA (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol 310:311-325
-
(2001)
J Mol Biol
, vol.310
, pp. 311-325
-
-
Apic, G.1
Gough, J.2
Teichmann, S.A.3
-
9
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
10
-
-
38349164409
-
Computing topological parameters of biological networks
-
Assenov Y, Ramirez F, Schelhorn SE, 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
-
11
-
-
0037245913
-
BIND: The Biomolecular interaction network database
-
Bader GD, Betel D, Hogue CW (2003) BIND: the Biomolecular interaction network database. Nucleic Acids Res 31:248-250
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.3
-
12
-
-
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
-
13
-
-
33845898805
-
Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes
-
Barker D, Meade A, Pagel M (2007) Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics 23:14-20
-
(2007)
Bioinformatics
, vol.23
, pp. 14-20
-
-
Barker, D.1
Meade, A.2
Pagel, M.3
-
14
-
-
55449127787
-
Predicting functional gene links from phylogenetic-statistical analyses of whole genomes
-
Barker D, Pagel M (2005) Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput Biol 1:e3
-
(2005)
PLoS Comput Biol
, vol.1
, pp. e3
-
-
Barker, D.1
Pagel, M.2
-
15
-
-
20144372620
-
High-throughput mapping of a dynamic signaling network in mammalian cells
-
Barrios-Rodiles M, Brown KR, Ozdamar B, Bose R, Liu Z, Donovan RS, Shinjo F, Liu Y, Dembowy J, Taylor IW, Luga V, Przulj N, Robinson M, Suzuki H, Hayashizaki Y, Jurisica I, Wrana JL (2005) High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307:1621-1625
-
(2005)
Science
, vol.307
, pp. 1621-1625
-
-
Barrios-Rodiles, M.1
Brown, K.R.2
Ozdamar, B.3
Bose, R.4
Liu, Z.5
Donovan, R.S.6
Shinjo, F.7
Liu, Y.8
Dembowy, J.9
Taylor, I.W.10
Luga, V.11
Przulj, N.12
Robinson, M.13
Suzuki, H.14
Hayashizaki, Y.15
Jurisica, I.16
Wrana, J.L.17
-
16
-
-
33846036096
-
The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
-
Berman H, Henrick K, Nakamura H, Markley JL (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35:D301-D303
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D301-D303
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
Markley, J.L.4
-
17
-
-
0035023445
-
Predicting protein-protein interactions from primary structure
-
Bock JR, Gough DA (2001) Predicting protein-protein interactions from primary structure. Bioinformatics 17:455-460
-
(2001)
Bioinformatics
, vol.17
, pp. 455-460
-
-
Bock, J.R.1
Gough, D.A.2
-
18
-
-
0345863927
-
The Unified Medical Language System (UMLS): Integrating biomedical terminology
-
Bodenreider O (2004) The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res 32:D267-D270
-
(2004)
Nucleic Acids Res
, vol.32
, pp. D267-D270
-
-
Bodenreider, O.1
-
19
-
-
12144289400
-
A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway
-
Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, Croughton K, Cruciat C, Eberhard D, Gagneur J, Ghidelli S, Hopf C, Huhse B, Mangano R, Michon AM, Schirle M, Schlegl J, Schwab M, Stein MA, Bauer A, Casari G, Drewes G, Gavin AC, Jackson DB, Joberty G, Neubauer G, Rick J, Kuster B, Superti-Furga G (2004) A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 6:97-105
-
(2004)
Nat Cell Biol
, vol.6
, pp. 97-105
-
-
Bouwmeester, T.1
Bauch, A.2
Ruffner, H.3
Angrand, P.O.4
Bergamini, G.5
Croughton, K.6
Cruciat, C.7
Eberhard, D.8
Gagneur, J.9
Ghidelli, S.10
Hopf, C.11
Huhse, B.12
Mangano, R.13
Michon, A.M.14
Schirle, M.15
Schlegl, J.16
Schwab, M.17
Stein, M.A.18
Bauer, A.19
Casari, G.20
Drewes, G.21
Gavin, A.C.22
Jackson, D.B.23
Joberty, G.24
Neubauer, G.25
Rick, J.26
Kuster, B.27
Superti-Furga, G.28
more..
-
20
-
-
11144319853
-
Use of logic relationships to decipher protein network organization
-
Bowers PM, Cokus SJ, Eisenberg D, Yeates TO (2004) Use of logic relationships to decipher protein network organization. Science 306:2246-2249
-
(2004)
Science
, vol.306
, pp. 2246-2249
-
-
Bowers, P.M.1
Cokus, S.J.2
Eisenberg, D.3
Yeates, T.O.4
-
21
-
-
0037264524
-
The GRID: The general repository for interaction datasets
-
Breitkreutz BJ, Stark C, Tyers M (2003) The GRID: the General Repository for Interaction Datasets. Genome Biol 4:R23
-
(2003)
Genome Biol
, vol.4
, pp. R23
-
-
Breitkreutz, B.J.1
Stark, C.2
Tyers, M.3
-
22
-
-
13444283630
-
Interaction network containing conserved and essential protein complexes in Escherichia coli
-
Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433:531-537
-
(2005)
Nature
, vol.433
, pp. 531-537
-
-
Butland, G.1
Peregrin-Alvarez, J.M.2
Li, J.3
Yang, W.4
Yang, X.5
Canadien, V.6
Starostine, A.7
Richards, D.8
Beattie, B.9
Krogan, N.10
Davey, M.11
Parkinson, J.12
Greenblatt, J.13
Emili, A.14
-
23
-
-
34250675300
-
Epstein-Barr virus and virus human protein interaction maps
-
Calderwood MA, Venkatesan K, Xing L, Chase MR, Vazquez A, Holthaus AM, Ewence AE, Li N, Hirozane-Kishikawa T, Hill DE, Vidal M, Kieff E, Johannsen E (2007) Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci USA 104:7606-7611
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 7606-7611
-
-
Calderwood, M.A.1
Venkatesan, K.2
Xing, L.3
Chase, M.R.4
Vazquez, A.5
Holthaus, A.M.6
Ewence, A.E.7
Li, N.8
Hirozane-Kishikawa, T.9
Hill, D.E.10
Vidal, M.11
Kieff, E.12
Johannsen, E.13
-
24
-
-
27144509163
-
A network-based analysis of systemic inflammation in humans
-
Calvano SE, Xiao W, Richards DR, Felciano RM, Baker HV, Cho RJ, Chen RO, Brownstein BH, Cobb JP, Tschoeke SK, Miller-Graziano C, Moldawer LL, Mindrinos MN, Davis RW, Tompkins RG, Lowry SF (2005) A network-based analysis of systemic inflammation in humans. Nature 437:1032-1037
-
(2005)
Nature
, vol.437
, pp. 1032-1037
-
-
Calvano, S.E.1
Xiao, W.2
Richards, D.R.3
Felciano, R.M.4
Baker, H.V.5
Cho, R.J.6
Chen, R.O.7
Brownstein, B.H.8
Cobb, J.P.9
Tschoeke, S.K.10
Miller-Graziano, C.11
Moldawer, L.L.12
Mindrinos, M.N.13
Davis, R.W.14
Tompkins, R.G.15
Lowry, S.F.16
-
25
-
-
33845748185
-
Disrupted in Schizophrenia 1 Interactome: Evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia
-
Camargo LM, Collura V, Rain JC, Mizuguchi K, Hermjakob H, Kerrien S, Bonnert TP, Whiting PJ, Brandon NJ (2006) Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia. Mol Psychiatry 12:74-86
-
(2006)
Mol Psychiatry
, vol.12
, pp. 74-86
-
-
Camargo, L.M.1
Collura, V.2
Rain, J.C.3
Mizuguchi, K.4
Hermjakob, H.5
Kerrien, S.6
Bonnert, T.P.7
Whiting, P.J.8
Brandon, N.J.9
-
26
-
-
0036019065
-
Protein flexibility is an important component of structure-based drug discovery
-
Carlson HA (2002) Protein flexibility is an important component of structure-based drug discovery. Curr Pharm Des 8:1571-1578
-
(2002)
Curr Pharm des
, vol.8
, pp. 1571-1578
-
-
Carlson, H.A.1
-
27
-
-
33846073818
-
MINT: The Molecular INTeraction database
-
Chatr-Aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res 35:D572-D574
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D572-D574
-
-
Chatr-Aryamontri, A.1
Ceol, A.2
Palazzi, L.M.3
Nardelli, G.4
Schneider, M.V.5
Castagnoli, L.6
Cesareni, G.7
-
28
-
-
33244483907
-
On evaluating molecular-docking methods for pose prediction and enrichment factors
-
Chen H, Lyne PD, Giordanetto F, Lovell T, Li J (2006) On evaluating molecular-docking methods for pose prediction and enrichment factors. J Chem Inf Model 46:401-415
-
(2006)
J Chem Inf Model
, vol.46
, pp. 401-415
-
-
Chen, H.1
Lyne, P.D.2
Giordanetto, F.3
Lovell, T.4
Li, J.5
-
29
-
-
28944450149
-
Prediction of protein-protein interactions using random decision forest framework
-
Chen XW, Liu M (2005) Prediction of protein-protein interactions using random decision forest framework. Bioinformatics 21:4394-4400
-
(2005)
Bioinformatics
, vol.21
, pp. 4394-4400
-
-
Chen, X.W.1
Liu, M.2
-
30
-
-
33746255908
-
The coordinated evolutionof yeast proteins is constrained byfunctional modularity
-
Chen Y, Dokholyan NV (2006) The coordinated evolutionof yeast proteins is constrained byfunctional modularity. Trends Genet 22:416-419
-
(2006)
Trends Genet
, vol.22
, pp. 416-419
-
-
Chen, Y.1
Dokholyan, N.V.2
-
31
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang HY, Lee E, Liu YT, Lee D, Ideker T (2007) Network-based classification of breast cancer metastasis. Mol Syst Biol 3:140
-
(2007)
Mol Syst Biol
, vol.3
, pp. 140
-
-
Chuang, H.Y.1
Lee, E.2
Liu, Y.T.3
Lee, D.4
Ideker, T.5
-
32
-
-
0035957528
-
FlexE: Efficient molecular docking considering protein structure variations
-
Claußen H, Buning C, Rarey M, Lengauer T (2001) FlexE: efficient molecular docking considering protein structure variations. J Mol Biol 308:377-395
-
(2001)
J Mol Biol
, vol.308
, pp. 377-395
-
-
Claußen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
33
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366-2382
-
(2007)
Nat Protoc
, vol.2
, pp. 2366-2382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
Kuchinsky, A.4
Landys, N.5
Workman, C.6
Christmas, R.7
Avila-Campilo, I.8
Creech, M.9
Gross, B.10
Hanspers, K.11
Isserlin, R.12
Kelley, R.13
Killcoyne, S.14
Lotia, S.15
Maere, S.16
Morris, J.17
Ono, K.18
Pavlovic, V.19
Pico, A.R.20
Vailaya, A.21
Wang, P.L.22
Adler, A.23
Conklin, B.R.24
Hood, L.25
Kuiper, M.26
Sander, C.27
Schmulevich, I.28
Schwikowski, B.29
Warner, G.J.30
Ideker, T.31
Bader, G.D.32
more..
-
34
-
-
8844280078
-
Integrating a functional proteomic approach into the target discovery process
-
Colland F, Daviet L (2004) Integrating a functional proteomic approach into the target discovery process. Biochimie 86:625-632
-
(2004)
Biochimie
, vol.86
, pp. 625-632
-
-
Colland, F.1
Daviet, L.2
-
35
-
-
0034907351
-
Identification of the Helicobacter pylori anti-sigma28 factor
-
Colland F, Rain JC, Gounon P, Labigne A, Legrain P, De Reuse H (2001) Identification of the Helicobacter pylori anti-sigma28 factor. Mol Microbiol 41:477-487
-
(2001)
Mol Microbiol
, vol.41
, pp. 477-487
-
-
Colland, F.1
Rain, J.C.2
Gounon, P.3
Labigne, A.4
Legrain, P.5
De Reuse, H.6
-
36
-
-
37349068664
-
A map of human cancer signaling
-
Cui Q, Ma Y, Jaramillo M, Bari H, Awan A, Yang S, Zhang S, Liu L, Lu M, O'Connor-McCourt M, Purisima EO, Wang E (2007) A map of human cancer signaling. Mol Syst Biol 3:152
-
(2007)
Mol Syst Biol
, vol.3
, pp. 152
-
-
Cui, Q.1
Ma, Y.2
Jaramillo, M.3
Bari, H.4
Awan, A.5
Yang, S.6
Zhang, S.7
Liu, L.8
Lu, M.9
O'Connor-Mc Court, M.10
Purisima, E.O.11
Wang, E.12
-
38
-
-
0032169271
-
Conservation of gene order: A fingerprintof proteins that physically interact
-
Dandekar T, Snel B, Huynen M, Bork P (1998) Conservation of gene order: a fingerprintof proteins that physically interact. Trends Biochem Sci 23:324-328
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
39
-
-
0041358614
-
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
-
Date SV, Marcotte EM (2003) Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol 21:1055-1062
-
(2003)
Nat Biotechnol
, vol.21
, pp. 1055-1062
-
-
Date, S.V.1
Marcotte, E.M.2
-
40
-
-
0036799752
-
Inferring domain-domain interactions from protein-protein interactions
-
Deng M, Mehta S, Sun F, Chen T (2002) Inferring domain-domain interactions from protein-protein interactions. Genome Res 12:1540-1548
-
(2002)
Genome Res
, vol.12
, pp. 1540-1548
-
-
Deng, M.1
Mehta, S.2
Sun, F.3
Chen, T.4
-
41
-
-
27144464910
-
Flexible nets. The roles of intrinsic disorder in protein interaction networks
-
Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN (2005) Flexible nets. The roles of intrinsic disorder in protein interaction networks. 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
-
42
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755-763
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
43
-
-
34548304863
-
Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: A comparison with crystallography
-
Englebienne P, Fiaux H, Kuntz DA, Corbeil CR, Gerber-Lemaire S, Rose DR, Moitessier N (2007) Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography. Proteins 69:160-176
-
(2007)
Proteins
, vol.69
, pp. 160-176
-
-
Englebienne, P.1
Fiaux, H.2
Kuntz, D.A.3
Corbeil, C.R.4
Gerber-Lemaire, S.5
Rose, D.R.6
Moitessier, N.7
-
44
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86-90
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
45
-
-
0024406857
-
A novel genetic system to detect protein-protein interactions
-
Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340:245-246
-
(1989)
Nature
, vol.340
, pp. 245-246
-
-
Fields, S.1
Song, O.2
-
46
-
-
13844264506
-
IPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions
-
Finn RD, Marshall M, Bateman A (2005) iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 21:410-412
-
(2005)
Bioinformatics
, vol.21
, pp. 410-412
-
-
Finn, R.D.1
Marshall, M.2
Bateman, A.3
-
47
-
-
33644876020
-
Pfam: Clans, web tools and services
-
Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247-D251
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D247-D251
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Bockler, B.3
Griffiths-Jones, S.4
Hollich, V.5
Lassmann, T.6
Moxon, S.7
Marshall, M.8
Khanna, A.9
Durbin, R.10
Eddy, S.R.11
Sonnhammer, E.L.12
Bateman, A.13
-
48
-
-
25644454404
-
Pharmaceuticals: A new grammar for drug discovery
-
Fishman MC, Porter JA (2005) Pharmaceuticals: a new grammar for drug discovery. Nature 437:491-493
-
(2005)
Nature
, vol.437
, pp. 491-493
-
-
Fishman, M.C.1
Porter, J.A.2
-
49
-
-
0033978737
-
A genomic approach of the hepatitis C virus generates a protein interaction map
-
Flajolet M, Rotondo G, Daviet L, Bergametti F, Inchauspe G, Tiollais P, Transy C, Legrain P (2000) A genomic approach of the hepatitis C virus generates a protein interaction map. Gene 242:369-379
-
(2000)
Gene
, vol.242
, pp. 369-379
-
-
Flajolet, M.1
Rotondo, G.2
Daviet, L.3
Bergametti, F.4
Inchauspe, G.5
Tiollais, P.6
Transy, C.7
Legrain, P.8
-
50
-
-
33646884801
-
Reconstruction ofa functional human gene network, with an application for prioritizing positional candidate genes
-
Franke L, Bakel H, Fokkens L, De Jong ED, Egmont-Petersen M, Wijmenga C (2006) Reconstruction ofa functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet 78:1011-1025
-
(2006)
Am J Hum Genet
, vol.78
, pp. 1011-1025
-
-
Franke, L.1
Bakel, H.2
Fokkens, L.3
De Jong, E.D.4
Egmont-Petersen, M.5
Wijmenga, C.6
-
51
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-1749
-
(2004)
J Med Chem
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
52
-
-
0030249746
-
The coevolution of gene family trees
-
Fryxell KJ (1996) The coevolution of gene family trees. Trends Genet 12:364-369
-
(1996)
Trends Genet
, vol.12
, pp. 364-369
-
-
Fryxell, K.J.1
-
53
-
-
0032242111
-
Microbial genescapes: Phyletic and functional patterns of ORF distribution among prokaryotes
-
Gaasterland T, Ragan MA (1998) Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microb Comp Genomics 3:199-217
-
(1998)
Microb Comp Genomics
, vol.3
, pp. 199-217
-
-
Gaasterland, T.1
Ragan, M.A.2
-
54
-
-
33644617753
-
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
-
Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38:285-293
-
(2006)
Nat Genet
, vol.38
, pp. 285-293
-
-
Gandhi, T.K.1
Zhong, J.2
Mathivanan, S.3
Karthick, L.4
Chandrika, K.N.5
Mohan, S.S.6
Sharma, S.7
Pinkert, S.8
Nagaraju, S.9
Periaswamy, B.10
Mishra, G.11
Nandakumar, K.12
Shen, B.13
Deshpande, N.14
Nayak, R.15
Sarker, M.16
Boeke, J.D.17
Parmigiani, G.18
Schultz, J.19
Bader, J.S.20
Pandey, A.21
more..
-
55
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G (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
Marzioch, M.6
Rau, C.7
Jensen, L.J.8
Bastuck, S.9
Dumpelfeld, B.10
Edelmann, A.11
Heurtier, M.A.12
Hoffman, V.13
Hoefert, C.14
Klein, K.15
Hudak, M.16
Michon, A.M.17
Schelder, M.18
Schirle, M.19
Remor, M.20
Rudi, T.21
Hooper, S.22
Bauer, A.23
Bouwmeester, T.24
Casari, G.25
Drewes, G.26
Neubauer, G.27
Rick, J.M.28
Kuster, B.29
Bork, P.30
Russell, R.B.31
Superti-Furga, G.32
more..
-
56
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (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
Bauer, A.6
Schultz, J.7
Rick, J.M.8
Michon, A.M.9
Cruciat, C.M.10
Remor, M.11
Hofert, C.12
Schelder, M.13
Brajenovic, M.14
Ruffner, H.15
Merino, A.16
Klein, K.17
Hudak, M.18
Dickson, D.19
Rudi, T.20
Gnau, V.21
Bauch, A.22
Bastuck, S.23
Huhse, B.24
Leutwein, C.25
Heurtier, M.A.26
Copley, R.R.27
Edelmann, A.28
Querfurth, E.29
Rybin, V.30
Drewes, G.31
Raida, M.32
Bouwmeester, T.33
Bork, P.34
Seraphin, B.35
Kuster, B.36
Neubauer, G.37
Superti-Furga, G.38
more..
-
57
-
-
0141504252
-
Experimental determination and system level analysis of essential genes in Escherichia coli MG1655
-
Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185:5673-5684
-
(2003)
J Bacteriol
, vol.185
, pp. 5673-5684
-
-
Gerdes, S.Y.1
Scholle, M.D.2
Campbell, J.W.3
Balazsi, G.4
Ravasz, E.5
Daugherty, M.D.6
Somera, A.L.7
Kyrpides, N.C.8
Anderson, I.9
Gelfand, M.S.10
Bhattacharya, A.11
Kapatral, V.12
D'Souza, M.13
Baev, M.V.14
Grechkin, Y.15
Mseeh, F.16
Fonstein, M.Y.17
Overbeek, R.18
Barabasi, A.L.19
Oltvai, Z.N.20
Osterman, A.L.21
more..
-
58
-
-
0037173615
-
Functional profiling of the Saccharomyces cerevisiae genome
-
Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, La Bonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387-391
-
(2002)
Nature
, vol.418
, pp. 387-391
-
-
Giaever, G.1
Chu, A.M.2
Ni, L.3
Connelly, C.4
Riles, L.5
Veronneau, S.6
Dow, S.7
Lucau-Danila, A.8
Anderson, K.9
Andre, B.10
Arkin, A.P.11
Astromoff, A.12
El-Bakkoury, M.13
Bangham, R.14
Benito, R.15
Brachat, S.16
Campanaro, S.17
Curtiss, M.18
Davis, K.19
Deutschbauer, A.20
Entian, K.D.21
Flaherty, P.22
Foury, F.23
Garfinkel, D.J.24
Gerstein, M.25
Gotte, D.26
Guldener, U.27
Hegemann, J.H.28
Hempel, S.29
Herman, Z.30
Jaramillo, D.F.31
Kelly, D.E.32
Kelly, S.L.33
Kotter, P.34
La Bonte, D.35
Lamb, D.C.36
Lan, N.37
Liang, H.38
Liao, H.39
Liu, L.40
Luo, C.41
Lussier, M.42
Mao, R.43
Menard, P.44
Ooi, S.L.45
Revuelta, J.L.46
Roberts, C.J.47
Rose, M.48
Ross-Macdonald, P.49
Scherens, B.50
Schimmack, G.51
Shafer, B.52
Shoemaker, D.D.53
Sookhai-Mahadeo, S.54
Storms, R.K.55
Strathern, J.N.56
Valle, G.57
Voet, M.58
Volckaert, G.59
Wang, C.Y.60
Ward, T.R.61
Wilhelmy, J.62
Winzeler, E.A.63
Yang, Y.64
Yen, G.65
Youngman, E.66
Yu, K.67
Bussey, H.68
Boeke, J.D.69
Snyder, M.70
Philippsen, P.71
Davis, R.W.72
Johnston, M.73
more..
-
59
-
-
25844439570
-
Disease gene discovery through integrative genomics
-
Giallourakis C, Henson C, Reich M, Xie X, Mootha VK (2005) Disease gene discovery through integrative genomics. Annu Rev Genomics Hum Genet 6:381-406
-
(2005)
Annu Rev Genomics Hum Genet
, vol.6
, pp. 381-406
-
-
Giallourakis, C.1
Henson, C.2
Reich, M.3
Xie, X.4
Mootha, V.K.5
-
61
-
-
0345600247
-
A protein interaction map of Drosophila melanogaster
-
Giot L (2003) A protein interaction map of Drosophila melanogaster. Science 302:1727-1736
-
(2003)
Science
, vol.302
, pp. 1727-1736
-
-
Giot, L.1
-
62
-
-
4644231870
-
A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease
-
Goehler H, Lalowski M, Stelzl U, Waelter S, Stroedicke M, Worm U, Droege A, Lindenberg KS, Knoblich M, Haenig C, Herbst M, Suopanki J, Scherzinger E, Abraham C, Bauer B, Hasenbank R, Fritzsche A, Ludewig AH, Bussow K, Coleman SH, Gutekunst CA, Landwehrmeyer BG, Lehrach H, Wanker EE (2004) A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell 15:853-865
-
(2004)
Mol Cell
, vol.15
, pp. 853-865
-
-
Goehler, H.1
Lalowski, M.2
Stelzl, U.3
Waelter, S.4
Stroedicke, M.5
Worm, U.6
Droege, A.7
Lindenberg, K.S.8
Knoblich, M.9
Haenig, C.10
Herbst, M.11
Suopanki, J.12
Scherzinger, E.13
Abraham, C.14
Bauer, B.15
Hasenbank, R.16
Fritzsche, A.17
Ludewig, A.H.18
Bussow, K.19
Coleman, S.H.20
Gutekunst, C.A.21
Landwehrmeyer, B.G.22
Lehrach, H.23
Wanker, E.E.24
more..
-
63
-
-
0034595516
-
Co-evolution of proteins with their interaction partners
-
Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE (2000) Co-evolution of proteins with their interaction partners. J Mol Biol 299:283-293
-
(2000)
J Mol Biol
, vol.299
, pp. 283-293
-
-
Goh, C.S.1
Bogan, A.A.2
Joachimiak, M.3
Walther, D.4
Cohen, F.E.5
-
64
-
-
84889790228
-
Analyzing protein interaction networks
-
Lengauer T ed, Wiley-VCH, Weinheim
-
Goll J, Uetz P (2007) Analyzing Protein Interaction Networks. In: Lengauer T (ed) Bioinformatics - from genomes to therapies. Wiley-VCH, Weinheim, pp 1121-1179
-
(2007)
Bioinformatics - From Genomes to Therapies
, pp. 1121-1179
-
-
Goll, J.1
Uetz, P.2
-
65
-
-
34547140875
-
The human disease network
-
Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL (2007) The human disease network. Proc Natl Acad Sci USA 104:8685-8690
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 8685-8690
-
-
Goh, K.I.1
Cusick, M.E.2
Valle, D.3
Childs, B.4
Vidal, M.5
Barabasi, A.L.6
-
66
-
-
0036009331
-
MgF (3) (-) as a transition state analog of phosphoryl transfer
-
Graham DL, Lowe PN, Grime GW, Marsh M, Rittinger K, Smerdon SJ, Gamblin SJ, Eccleston JF (2002) MgF (3) (-) as a transition state analog of phosphoryl transfer. Chem Biol 9:375-381
-
(2002)
Chem Biol
, vol.9
, pp. 375-381
-
-
Graham, D.L.1
Lowe, P.N.2
Grime, G.W.3
Marsh, M.4
Rittinger, K.5
Smerdon, S.J.6
Gamblin, S.J.7
Eccleston, J.F.8
-
67
-
-
33846033844
-
The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution
-
Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA (2007) The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 35:D291-D297
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D291-D297
-
-
Greene, L.H.1
Lewis, T.E.2
Addou, S.3
Cuff, A.4
Dallman, T.5
Dibley, M.6
Redfern, O.7
Pearl, F.8
Nambudiry, R.9
Reid, A.10
Sillitoe, I.11
Yeats, C.12
Thornton, J.M.13
Orengo, C.A.14
-
68
-
-
33644878150
-
MPact: The MIPS protein interaction resource on yeast
-
Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V (2006) MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res 34:D436-D441
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D436-D441
-
-
Guldener, U.1
Munsterkotter, M.2
Oesterheld, M.3
Pagel, P.4
Ruepp, A.5
Mewes, H.W.6
Stumpflen, V.7
-
69
-
-
13444266370
-
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
-
Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33:D514-D517
-
(2005)
Nucleic Acids Res
, vol.33
, pp. D514-D517
-
-
Hamosh, A.1
Scott, A.F.2
Amberger, J.S.3
Bocchini, C.A.4
McKusick, V.A.5
-
70
-
-
13444301479
-
PreSPI: A domain combination based prediction system for protein-protein interaction
-
Han DS, Kim HS, Jang WH, Lee SD, Suh JK (2004) PreSPI: a domain combination based prediction system for protein-protein interaction. Nucleic Acids Res 32:6312-6320
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 6312-6320
-
-
Han, D.S.1
Kim, H.S.2
Jang, W.H.3
Lee, S.D.4
Suh, J.K.5
-
71
-
-
0346801873
-
The Gene Ontology (GO) database and informatics resource
-
Database issue
-
Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, De La Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32 (Database issue):D258-D261
-
(2004)
Nucleic Acids Res
, vol.32
, pp. D258-D261
-
-
Harris, M.A.1
Clark, J.2
Ireland, A.3
Lomax, J.4
Ashburner, M.5
Foulger, R.6
Eilbeck, K.7
Lewis, S.8
Marshall, B.9
Mungall, C.10
Richter, J.11
Rubin, G.M.12
Blake, J.A.13
Bult, C.14
Dolan, M.15
Drabkin, H.16
Eppig, J.T.17
Hill, D.P.18
Ni, L.19
Ringwald, M.20
Balakrishnan, R.21
Cherry, J.M.22
Christie, K.R.23
Costanzo, M.C.24
Dwight, S.S.25
Engel, S.26
Fisk, D.G.27
Hirschman, J.E.28
Hong, E.L.29
Nash, R.S.30
Sethuraman, A.31
Theesfeld, C.L.32
Botstein, D.33
Dolinski, K.34
Feierbach, B.35
Berardini, T.36
Mundodi, S.37
Rhee, S.Y.38
Apweiler, R.39
Barrell, D.40
Camon, E.41
Dimmer, E.42
Lee, V.43
Chisholm, R.44
Gaudet, P.45
Kibbe, W.46
Kishore, R.47
Schwarz, E.M.48
Sternberg, P.49
Gwinn, M.50
Hannick, L.51
Wortman, J.52
Berriman, M.53
Wood, V.54
De La Cruz, N.55
Tonellato, P.56
Jaiswal, P.57
Seigfried, T.58
White, R.59
more..
-
73
-
-
33745712594
-
Why do hubs tend to be essential in protein networks?
-
He X, Zhang J (2006) Why do hubs tend to be essential in protein networks? PLoS Genet 2:e88
-
(2006)
PLoS Genet
, vol.2
, pp. e88
-
-
He, X.1
Zhang, J.2
-
74
-
-
0742323374
-
The HUPO PSI's molecular interaction format - A community standard for the representation of protein interaction data
-
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, Von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R (2004) The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat Biotechnol 22:177-183
-
(2004)
Nat Biotechnol
, vol.22
, pp. 177-183
-
-
Hermjakob, H.1
Montecchi-Palazzi, L.2
Bader, G.3
Wojcik, J.4
Salwinski, L.5
Ceol, A.6
Moore, S.7
Orchard, S.8
Sarkans, U.9
Von Mering, C.10
Roechert, B.11
Poux, S.12
Jung, E.13
Mersch, H.14
Kersey, P.15
Lappe, M.16
Li, Y.17
Zeng, R.18
Rana, D.19
Nikolski, M.20
Husi, H.21
Brun, C.22
Shanker, K.23
Grant, S.G.24
Sander, C.25
Bork, P.26
Zhu, W.27
Pandey, A.28
Brazma, A.29
Jacq, B.30
Vidal, M.31
Sherman, D.32
Legrain, P.33
Cesareni, G.34
Xenarios, I.35
Eisenberg, D.36
Steipe, B.37
Hogue, C.38
Apweiler, R.39
more..
-
75
-
-
84889781360
-
Modeling protein-protein and protein-DNA docking
-
Lengauer T ed, Wiley-VCH, Weinheim
-
Hildebrandt A, Kohlbacher O, Lenhof H-P (2007) Modeling protein-protein and protein-DNA docking. In: Lengauer T (ed) Bioinformatics - from genomes to therapies. Wiley-VCH, Weinheim, pp 601-650
-
(2007)
Bioinformatics - From Genomes to Therapies
, pp. 601-650
-
-
Hildebrandt, A.1
Kohlbacher, O.2
Lenhof, H.-P.3
-
76
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183
-
(2002)
Nature
, vol.415
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
Bader, G.D.4
Moore, L.5
Adams, S.L.6
Millar, A.7
Taylor, P.8
Bennett, K.9
Boutilier, K.10
Yang, L.11
Wolting, C.12
Donaldson, I.13
Schandorff, S.14
Shewnarane, J.15
Vo, M.16
Taggart, J.17
Goudreault, M.18
Muskat, B.19
Alfarano, C.20
Dewar, D.21
Lin, Z.22
Michalickova, K.23
Willems, A.R.24
Sassi, H.25
Nielsen, P.A.26
Rasmussen, K.J.27
Andersen, J.R.28
Johansen, L.E.29
Hansen, L.H.30
Jespersen, H.31
Podtelejnikov, A.32
Nielsen, E.33
Crawford, J.34
Poulsen, V.35
Sorensen, B.D.36
Matthiesen, J.37
Hendrickson, R.C.38
Gleeson, F.39
Pawson, T.40
Moran, M.F.41
Durocher, D.42
Mann, M.43
Hogue, C.W.44
Figeys, D.45
Tyers, M.46
more..
-
77
-
-
34249653071
-
Towards zoomable multidimensional maps of the cell
-
Hu Z, Mellor J, Wu J, Kanehisa M, Stuart JM, De Lisi C (2007) Towards zoomable multidimensional maps of the cell. Nat Biotechnol 25:547-554
-
(2007)
Nat Biotechnol
, vol.25
, pp. 547-554
-
-
Hu, Z.1
Mellor, J.2
Wu, J.3
Kanehisa, M.4
Stuart, J.M.5
De Lisi, C.6
-
78
-
-
23144466889
-
VisANT: Data-integrating visual framework for biological networks and modules
-
Hu Z, Mellor J, Wu J, Yamada T, Holloway D, Delisi C (2005) VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res 33:W352-W357
-
(2005)
Nucleic Acids Res
, vol.33
, pp. W352-W357
-
-
Hu, Z.1
Mellor, J.2
Wu, J.3
Yamada, T.4
Holloway, D.5
Delisi, C.6
-
79
-
-
33750574927
-
An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function
-
Huang SY, Zou X (2006) An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J Comput Chem 27:1876-1882
-
(2006)
J Comput Chem
, vol.27
, pp. 1876-1882
-
-
Huang, S.Y.1
Zou, X.2
-
82
-
-
0142052944
-
A Bayesian networks approach for predicting protein-protein interactions from genomic data
-
Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302:449-453
-
(2003)
Science
, vol.302
, pp. 449-453
-
-
Jansen, R.1
Yu, H.2
Greenbaum, D.3
Kluger, Y.4
Krogan, N.J.5
Chung, S.6
Emili, A.7
Snyder, M.8
Greenblatt, J.F.9
Gerstein, M.10
-
84
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748
-
(1997)
J Mol Biol
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
85
-
-
30544449081
-
A quantitative protein interaction network for the ErbB receptors using protein microarrays
-
Jones RB, Gordus A, Krall JA, MacBeath G (2006) A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439:168-174
-
(2006)
Nature
, vol.439
, pp. 168-174
-
-
Jones, R.B.1
Gordus, A.2
Krall, J.A.3
MacBeath, G.4
-
86
-
-
33748706765
-
Global topological features of cancer proteins in the human interactome
-
Jonsson PF, Bates PA (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22:2291-2297
-
(2006)
Bioinformatics
, vol.22
, pp. 2291-2297
-
-
Jonsson, P.F.1
Bates, P.A.2
-
87
-
-
33748333117
-
Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions
-
Jothi R, Cherukuri PF, Tasneem A, Przytycka TM (2006) Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol 362:861-875
-
(2006)
J Mol Biol
, vol.362
, pp. 861-875
-
-
Jothi, R.1
Cherukuri, P.F.2
Tasneem, A.3
Przytycka, T.M.4
-
88
-
-
38949168935
-
High-confidence prediction of global interactomes based on genome-wide coevolutionary networks
-
Juan D, Pazos F, Valencia A (2008) High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci USA 105:934-939
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 934-939
-
-
Juan, D.1
Pazos, F.2
Valencia, A.3
-
89
-
-
34249715853
-
Huntingtin interacting proteins are genetic modifiers of neurodegeneration
-
Kaltenbach LS, Romero E, Becklin RR, Chettier R, Bell R, Phansalkar A, Strand A, Torcassi C, Savage J, Hurlburt A, Cha GH, Ukani L, Chepanoske CL, Zhen Y, Sahasrabudhe S, Olson J, Kurschner C, Ellerby LM, Peltier JM, Botas J, Hughes RE (2007) Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PLoS Genet 3:e82
-
(2007)
PLoS Genet
, vol.3
, pp. e82
-
-
Kaltenbach, L.S.1
Romero, E.2
Becklin, R.R.3
Chettier, R.4
Bell, R.5
Phansalkar, A.6
Strand, A.7
Torcassi, C.8
Savage, J.9
Hurlburt, A.10
Cha, G.H.11
Ukani, L.12
Chepanoske, C.L.13
Zhen, Y.14
Sahasrabudhe, S.15
Olson, J.16
Kurschner, C.17
Ellerby, L.M.18
Peltier, J.M.19
Botas, J.20
Hughes, R.E.21
more..
-
90
-
-
84889812737
-
Lead Identification by virtual screaning
-
Lengauer T ed, Wiley-VCH, Weinheim
-
Kämper A, Rognan D, Lengauer T (2007) Lead Identification by virtual screaning. In: Lengauer T (ed) Bioinformatics - from genomes to therapies. Wiley-VCH, Weinheim, pp 651-704
-
(2007)
Bioinformatics - From Genomes to Therapies
, pp. 651-704
-
-
Kämper, A.1
Rognan, D.2
Lengauer, T.3
-
91
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480-D484
-
(2008)
Nucleic Acids Res
, vol.36
, pp. D480-D484
-
-
Kanehisa, M.1
Araki, M.2
Goto, S.3
Hattori, M.4
Hirakawa, M.5
Itoh, M.6
Katayama, T.7
Kawashima, S.8
Okuda, S.9
Tokimatsu, T.10
Yamanishi, Y.11
-
92
-
-
36349010138
-
Protein interactions and disease: Computational approaches to uncover the etiology of diseases
-
Kann MG (2007) Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform 8:333-346
-
(2007)
Brief Bioinform
, vol.8
, pp. 333-346
-
-
Kann, M.G.1
-
93
-
-
34248513211
-
Predicting protein domain interactions from coevolution of conserved regions
-
Kann MG, Jothi R, Cherukuri PF, Przytycka TM (2007) Predicting protein domain interactions from coevolution of conserved regions. Proteins 67:811-820
-
(2007)
Proteins
, vol.67
, pp. 811-820
-
-
Kann, M.G.1
Jothi, R.2
Cherukuri, P.F.3
Przytycka, T.M.4
-
94
-
-
33846876695
-
Relating protein pharmacology by ligand chemistry
-
Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK (2007) Relating protein pharmacology by ligand chemistry. Nat Biotechnol 25:197-206
-
(2007)
Nat Biotechnol
, vol.25
, pp. 197-206
-
-
Keiser, M.J.1
Roth, B.L.2
Armbruster, B.N.3
Ernsberger, P.4
Irwin, J.J.5
Shoichet, B.K.6
-
95
-
-
4544367743
-
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
-
Kellenberger E, Rodrigo J, Muller P, Rognan D (2004) Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 57:225-242
-
(2004)
Proteins
, vol.57
, pp. 225-242
-
-
Kellenberger, E.1
Rodrigo, J.2
Muller, P.3
Rognan, D.4
-
96
-
-
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 (2007a) IntAct-open source resource for molecular interaction data. Nucleic Acids Res 35:D561-D565
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D561-D565
-
-
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..
-
97
-
-
35348976204
-
Broadening the horizon - Level 2.5 of the HUPO-PSI format for molecular interactions
-
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H (2007b) Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions. BMC Biol 5:44
-
(2007)
BMC Biol
, vol.5
, pp. 44
-
-
Kerrien, S.1
Orchard, S.2
Montecchi-Palazzi, L.3
Aranda, B.4
Quinn, A.F.5
Vinod, N.6
Bader, G.D.7
Xenarios, I.8
Wojcik, J.9
Sherman, D.10
Tyers, M.11
Salama, J.J.12
Moore, S.13
Ceol, A.14
Chatr-Aryamontri, A.15
Oesterheld, M.16
Stumpflen, V.17
Salwinski, L.18
Nerothin, J.19
Cerami, E.20
Cusick, M.E.21
Vidal, M.22
Gilson, M.23
Armstrong, J.24
Woollard, P.25
Hogue, C.26
Eisenberg, D.27
Cesareni, G.28
Apweiler, R.29
Hermjakob, H.30
more..
-
98
-
-
33847377573
-
A robustness-based approachtosystems-oriented drug design
-
Kitano H (2007) A robustness-based approachtosystems-oriented drug design. Nat Rev Drug Discov 6:202-210
-
(2007)
Nat Rev Drug Discov
, vol.6
, pp. 202-210
-
-
Kitano, H.1
-
99
-
-
21844471754
-
Systematic association ofgenes tophenotypes bygenome and literature mining
-
Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P (2005) Systematic association ofgenes tophenotypes bygenome and literature mining. PLoS Biol 3:e134
-
(2005)
PLoS Biol
, vol.3
, pp. e134
-
-
Korbel, J.O.1
Doerks, T.2
Jensen, L.J.3
Perez-Iratxeta, C.4
Kaczanowski, S.5
Hooper, S.D.6
Andrade, M.A.7
Bork, P.8
-
100
-
-
3042703044
-
Analysis of genomic context: Prediction of functional associations from conserved bidirectionally transcribed gene pairs
-
Korbel JO, Jensen LJ, Von Mering C, Bork P (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol 22:911-917
-
(2004)
Nat Biotechnol
, vol.22
, pp. 911-917
-
-
Korbel, J.O.1
Jensen, L.J.2
Von Mering, C.3
Bork, P.4
-
101
-
-
0042196198
-
Fast3Dmolecular superposition and similarity search indatabases of flexible molecules
-
Krämer A, Horn HW, Rice JE (2003) Fast3Dmolecular superposition and similarity search indatabases of flexible molecules. J Comput Aided Mol Des 17:13-18
-
(2003)
J Comput Aided Mol des
, vol.17
, pp. 13-18
-
-
Krämer, A.1
Horn, H.W.2
Rice, J.E.3
-
102
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF (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
Ignatchenko, A.6
Li, J.7
Pu, S.8
Datta, N.9
Tikuisis, A.P.10
Punna, T.11
Peregrin-Alvarez, J.M.12
Shales, M.13
Zhang, X.14
Davey, M.15
Robinson, M.D.16
Paccanaro, A.17
Bray, J.E.18
Sheung, A.19
Beattie, B.20
Richards, D.P.21
Canadien, V.22
Lalev, A.23
Mena, F.24
Wong, P.25
Starostine, A.26
Canete, M.M.27
Vlasblom, J.28
Wu, S.29
Orsi, C.30
Collins, S.R.31
Chandran, S.32
Haw, R.33
Rilstone, J.J.34
Gandi, K.35
Thompson, N.J.36
Musso, G.37
St Onge, P.38
Ghanny, S.39
Lam, M.H.40
Butland, G.41
Altaf-Ul, A.M.42
Kanaya, S.43
Shilatifard, A.44
O'Shea, E.45
Weissman, J.S.46
Ingles, C.J.47
Hughes, T.R.48
Parkinson, J.49
Gerstein, M.50
Wodak, S.J.51
Emili, A.52
Greenblatt, J.F.53
more..
-
103
-
-
38549130733
-
STITCH: Interaction networks of chemicals and proteins
-
Kuhn M, Von Mering C, Campillos M, Jensen LJ, Bork P (2008) STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res 36:D684-D688
-
(2008)
Nucleic Acids Res
, vol.36
, pp. D684-D688
-
-
Kuhn, M.1
Von Mering, C.2
Campillos, M.3
Jensen, L.J.4
Bork, P.5
-
104
-
-
27644484749
-
A protein interaction network of the malaria parasite Plasmodium falciparum
-
La Count DJ, Vignali M, Chettier R, Phansalkar A, Bell R, Hesselberth JR, Schoenfeld LW, Ota I, Sahasrabudhe S, Kurschner C, Fields S, Hughes RE (2005) A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 438:103-107
-
(2005)
Nature
, vol.438
, pp. 103-107
-
-
La Count, D.J.1
Vignali, M.2
Chettier, R.3
Phansalkar, A.4
Bell, R.5
Hesselberth, J.R.6
Schoenfeld, L.W.7
Ota, I.8
Sahasrabudhe, S.9
Kurschner, C.10
Fields, S.11
Hughes, R.E.12
-
105
-
-
33947095027
-
A human phenome-interactome network of protein complexes implicated in genetic disorders
-
Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, Moreau Y, Brunak S (2007) A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 25:309-316
-
(2007)
Nat Biotechnol
, vol.25
, pp. 309-316
-
-
Lage, K.1
Karlberg, E.O.2
Storling, Z.M.3
Olason, P.I.4
Pedersen, A.G.5
Rigina, O.6
Hinsby, A.M.7
Tumer, Z.8
Pociot, F.9
Tommerup, N.10
Moreau, Y.11
Brunak, S.12
-
106
-
-
0034714420
-
Genome-wide protein interaction maps using two-hybrid systems
-
Legrain P, Selig L (2000) Genome-wide protein interaction maps using two-hybrid systems. FEBS Lett 480:32-36
-
(2000)
FEBS Lett
, vol.480
, pp. 32-36
-
-
Legrain, P.1
Selig, L.2
-
107
-
-
0032488013
-
FLEXS: A method for fast flexible ligand superposition
-
Lemmen C, Lengauer T, Klebe G (1998) FLEXS: a method for fast flexible ligand superposition. J Med Chem 41:4502-4520
-
(1998)
J Med Chem
, vol.41
, pp. 4502-4520
-
-
Lemmen, C.1
Lengauer, T.2
Klebe, G.3
-
109
-
-
33644877451
-
SMART 5: Domains in the context of genomes and networks
-
Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Res 34:D257-D260
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D257-D260
-
-
Letunic, I.1
Copley, R.R.2
Pils, B.3
Pinkert, S.4
Schultz, J.5
Bork, P.6
-
110
-
-
33646687963
-
A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration
-
Lim J, Hao T, Shaw C, Patel AJ, Szabo G, Rual JF, Fisk CJ, Li N, Smolyar A, Hill DE, Barabasi AL, Vidal M, Zoghbi HY (2006) A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125:801-814
-
(2006)
Cell
, vol.125
, pp. 801-814
-
-
Lim, J.1
Hao, T.2
Shaw, C.3
Patel, A.J.4
Szabo, G.5
Rual, J.F.6
Fisk, C.J.7
Li, N.8
Smolyar, A.9
Hill, D.E.10
Barabasi, A.L.11
Vidal, M.12
Zoghbi, H.Y.13
-
111
-
-
34548388340
-
Amultidimensional analysis ofgenes mutated in breast and colorectal cancers
-
Lin J, Gan CM, Zhang X, Jones S, Sjoblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, Parmigiani G, Velculescu VE (2007) Amultidimensional analysis ofgenes mutated in breast and colorectal cancers. Genome Res 17:1304-1318
-
(2007)
Genome Res
, vol.17
, pp. 1304-1318
-
-
Lin, J.1
Gan, C.M.2
Zhang, X.3
Jones, S.4
Sjoblom, T.5
Wood, L.D.6
Parsons, D.W.7
Papadopoulos, N.8
Kinzler, K.W.9
Vogelstein, B.10
Parmigiani, G.11
Velculescu, V.E.12
-
112
-
-
34347326247
-
Network-based analysis of affected biological processes in type 2 diabetes models
-
Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S (2007) Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet 3:e96
-
(2007)
PLoS Genet
, vol.3
, pp. e96
-
-
Liu, M.1
Liberzon, A.2
Kong, S.W.3
Lai, W.R.4
Park, P.J.5
Kohane, I.S.6
Kasif, S.7
-
113
-
-
34447521460
-
Human disease classification in the postgenomic era: A complex systems approach to human pathobiology
-
Loscalzo J, Kohane I, Barabasi AL (2007) Human disease classification in the postgenomic era: a complex systems approach to human pathobiology. Mol Syst Biol 3:124
-
(2007)
Mol Syst Biol
, vol.3
, pp. 124
-
-
Loscalzo, J.1
Kohane, I.2
Barabasi, A.L.3
-
114
-
-
34247217200
-
Hubsin biological interaction networks exhibit low changes in expression in experimental asthma
-
Lu X, Jain VV, Finn PW, Perkins DL (2007) Hubsin biological interaction networks exhibit low changes in expression in experimental asthma. Mol Syst Biol 3:98
-
(2007)
Mol Syst Biol
, vol.3
, pp. 98
-
-
Lu, X.1
Jain, V.V.2
Finn, P.W.3
Perkins, D.L.4
-
115
-
-
33846033400
-
CDD: A conserved domain database for interactive domain family analysis
-
Marchler-Bauer A, Anderson JB, Derbyshire MK, De Weese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 35:D237-D240
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D237-D240
-
-
Marchler-Bauer, A.1
Anderson, J.B.2
Derbyshire, M.K.3
De Weese-Scott, C.4
Gonzales, N.R.5
Gwadz, M.6
Hao, L.7
He, S.8
Hurwitz, D.I.9
Jackson, J.D.10
Ke, Z.11
Krylov, D.12
Lanczycki, C.J.13
Liebert, C.A.14
Liu, C.15
Lu, F.16
Lu, S.17
Marchler, G.H.18
Mullokandov, M.19
Song, J.S.20
Thanki, N.21
Yamashita, R.A.22
Yin, J.J.23
Zhang, D.24
Bryant, S.H.25
more..
-
116
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D (1999a) Detecting protein function and protein-protein interactions from genome sequences. Science 285:751-753
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
117
-
-
0033523854
-
A combined algorithm for genome-wide prediction of protein function
-
Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D (1999b) A combined algorithm for genome-wide prediction of protein function. Nature 402:83-86
-
(1999)
Nature
, vol.402
, pp. 83-86
-
-
Marcotte, E.M.1
Pellegrini, M.2
Thompson, M.J.3
Yeates, T.O.4
Eisenberg, D.5
-
118
-
-
0033523854
-
A combined algorithm for genome-wide prediction of protein function [see comments]
-
Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D (1999c) A combined algorithm for genome-wide prediction of protein function [see comments]. Nature 402:83-86
-
(1999)
Nature
, vol.402
, pp. 83-86
-
-
Marcotte, E.M.1
Pellegrini, M.2
Thompson, M.J.3
Yeates, T.O.4
Eisenberg, D.5
-
119
-
-
0346665839
-
Gaussian docking functions
-
McGann MR, Almond HR, Nicholls A, Grant JA, Brown FK (2003) Gaussian docking functions. Biopolymers 68:76-90
-
(2003)
Biopolymers
, vol.68
, pp. 76-90
-
-
McGann, M.R.1
Almond, H.R.2
Nicholls, A.3
Grant, J.A.4
Brown, F.K.5
-
120
-
-
0033127029
-
Pharmacophore fingerprinting. 1. Application to QSAR and focused library design
-
McGregor MJ, Muskal SM (1999) Pharmacophore fingerprinting. 1. Application to QSAR and focused library design. J Chem Inf Comput Sci 39:569-574
-
(1999)
J Chem Inf Comput Sci
, vol.39
, pp. 569-574
-
-
McGregor, M.J.1
Muskal, S.M.2
-
121
-
-
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 USA 102:10930-10935
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
122
-
-
33644877439
-
Human protein reference database-2006 update
-
Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, Menon S, Hanumanthu G, Gupta M, Upendran S, Gupta S, Mahesh M, Jacob B, Mathew P, Chatterjee P, Arun KS, Sharma S, Chandrika KN, Deshpande N, Palvankar K, Raghavnath R, Krishnakanth R, Karathia H, Rekha B, Nayak R, Vishnupriya G, Kumar HG, Nagini M, Kumar GS, Jose R, Deepthi P, Mohan SS, Gandhi TK, Harsha HC, Deshpande KS, Sarker M, Prasad TS, Pandey A (2006) Human protein reference database-2006 update. Nucleic Acids Res 34:D411-D414
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D411-D414
-
-
Mishra, G.R.1
Suresh, M.2
Kumaran, K.3
Kannabiran, N.4
Suresh, S.5
Bala, P.6
Shivakumar, K.7
Anuradha, N.8
Reddy, R.9
Raghavan, T.M.10
Menon, S.11
Hanumanthu, G.12
Gupta, M.13
Upendran, S.14
Gupta, S.15
Mahesh, M.16
Jacob, B.17
Mathew, P.18
Chatterjee, P.19
Arun, K.S.20
Sharma, S.21
Chandrika, K.N.22
Deshpande, N.23
Palvankar, K.24
Raghavnath, R.25
Krishnakanth, R.26
Karathia, H.27
Rekha, B.28
Nayak, R.29
Vishnupriya, G.30
Kumar, H.G.31
Nagini, M.32
Kumar, G.S.33
Jose, R.34
Deepthi, P.35
Mohan, S.S.36
Gandhi, T.K.37
Harsha, H.C.38
Deshpande, K.S.39
Sarker, M.40
Prasad, T.S.41
Pandey, A.42
more..
-
123
-
-
0037715424
-
Systematic discovery of analogous enzymes in thiamin biosynthesis
-
Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P (2003) Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol 21:790-795
-
(2003)
Nat Biotechnol
, vol.21
, pp. 790-795
-
-
Morett, E.1
Korbel, J.O.2
Rajan, E.3
Saab-Rincon, G.4
Olvera, L.5
Olvera, M.6
Schmidt, S.7
Snel, B.8
Bork, P.9
-
124
-
-
11644261806
-
Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function
-
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J Compu Chem 19:1639-1662
-
(1998)
J Compu Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
125
-
-
33846116032
-
New developments in the InterPro database
-
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C (2007) New developments in the InterPro database. Nucleic Acids Res 35:D224-D228
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D224-D228
-
-
Mulder, N.J.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Bork, P.7
Buillard, V.8
Cerutti, L.9
Copley, R.10
Courcelle, E.11
Das, U.12
Daugherty, L.13
Dibley, M.14
Finn, R.15
Fleischmann, W.16
Gough, J.17
Haft, D.18
Hulo, N.19
Hunter, S.20
Kahn, D.21
Kanapin, A.22
Kejariwal, A.23
Labarga, A.24
Langendijk-Genevaux, P.S.25
Lonsdale, D.26
Lopez, R.27
Letunic, I.28
Madera, M.29
Maslen, J.30
McAnulla, C.31
McDowall, J.32
Mistry, J.33
Mitchell, A.34
Nikolskaya, A.N.35
Orchard, S.36
Orengo, C.37
Petryszak, R.38
Selengut, J.D.39
Sigrist, C.J.40
Thomas, P.D.41
Valentin, F.42
Wilson, D.43
Wu, C.H.44
Yeats, C.45
more..
-
126
-
-
29144455315
-
Systematic discovery of new recognition peptides mediating protein interaction networks
-
Neduva V, Linding R, Su-Angrand I, Stark A, De Masi F, Gibson TJ, Lewis J, Serrano L, Russell RB (2005) Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol 3:e405
-
(2005)
PLoS Biol
, vol.3
, pp. e405
-
-
Neduva, V.1
Linding, R.2
Su-Angrand, I.3
Stark, A.4
De Masi, F.5
Gibson, T.J.6
Lewis, J.7
Serrano, L.8
Russell, R.B.9
-
127
-
-
0038620469
-
Integrative approach for computationally inferring protein domain interactions
-
Ng SK, Zhang Z, Tan SH (2003a) Integrative approach for computationally inferring protein domain interactions. Bioinformatics 19:923-929
-
(2003)
Bioinformatics
, vol.19
, pp. 923-929
-
-
Ng, S.K.1
Zhang, Z.2
Tan, S.H.3
-
128
-
-
0037250151
-
InterDom: A database of putative interacting protein domains for validating predicted protein interactions and complexes
-
Ng SK, Zhang Z, Tan SH, Lin K (2003b) InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res 31:251-254
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 251-254
-
-
Ng, S.K.1
Zhang, Z.2
Tan, S.H.3
Lin, K.4
-
129
-
-
23044515498
-
The solution structure of the Josephin domain of ataxin-3: Structural determinants for molecular recognition
-
Nicastro G, Menon RP, Masino L, Knowles PP, McDonald NQ, Pastore A (2005) The solution structure of the Josephin domain of ataxin-3: structural determinants for molecular recognition. Proc Natl Acad Sci USA 102:10493-10498
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10493-10498
-
-
Nicastro, G.1
Menon, R.P.2
Masino, L.3
Knowles, P.P.4
McDonald, N.Q.5
Pastore, A.6
-
131
-
-
0041312697
-
Diversity of protein-protein interactions
-
Nooren IM, Thornton JM (2003) Diversity of protein-protein interactions. EMBO J 22:3486-3492
-
(2003)
EMBO J
, vol.22
, pp. 3486-3492
-
-
Nooren, I.M.1
Thornton, J.M.2
-
132
-
-
33745463739
-
A comprehensive map of the toll-like receptor signaling network
-
Oda K, Kitano H (2006) A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol 2:2006 0015
-
(2006)
Mol Syst Biol
, vol.2
, pp. 2006-0015
-
-
Oda, K.1
Kitano, H.2
-
133
-
-
33746889808
-
A comprehensive pathway map of epidermal growth factor receptor signaling
-
Oda K, Matsuoka Y, Funahashi A, Kitano H (2005) A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 1:2005 0010
-
(2005)
Mol Syst Biol
, vol.1
, pp. 2005-0010
-
-
Oda, K.1
Matsuoka, Y.2
Funahashi, A.3
Kitano, H.4
-
134
-
-
41649106470
-
Submit your interaction data the IMEx way: A step by step guide to trouble-free deposition
-
Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H (2007a) Submit Your Interaction Data the IMEx Way: a Step by Step Guide to Trouble-free Deposition. Proteomics: 28-34
-
(2007)
Proteomics
, pp. 28-34
-
-
Orchard, S.1
Kerrien, S.2
Jones, P.3
Ceol, A.4
Chatr-Aryamontri, A.5
Salwinski, L.6
Nerothin, J.7
Hermjakob, H.8
-
135
-
-
34249107988
-
The minimum information required for reporting a molecular interaction experiment (MIMIx)
-
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatraryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H (2007b) The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol 25:894-898
-
(2007)
Nat Biotechnol
, vol.25
, pp. 894-898
-
-
Orchard, S.1
Salwinski, L.2
Kerrien, S.3
Montecchi-Palazzi, L.4
Oesterheld, M.5
Stumpflen, V.6
Ceol, A.7
Chatraryamontri, A.8
Armstrong, J.9
Woollard, P.10
Salama, J.J.11
Moore, S.12
Wojcik, J.13
Bader, G.D.14
Vidal, M.15
Cusick, M.E.16
Gerstein, M.17
Gavin, A.C.18
Superti-Furga, G.19
Greenblatt, J.20
Bader, J.21
Uetz, P.22
Tyers, M.23
Legrain, P.24
Fields, S.25
Mulder, N.26
Gilson, M.27
Niepmann, M.28
Burgoon, L.29
De Las Rivas, J.30
Prieto, C.31
Perreau, V.M.32
Hogue, C.33
Mewes, H.W.34
Apweiler, R.35
Xenarios, I.36
Eisenberg, D.37
Cesareni, G.38
Hermjakob, H.39
more..
-
136
-
-
22244450719
-
Protein families and their evolution-a structural perspective
-
Orengo CA, Thornton JM (2005) Protein families and their evolution-a structural perspective. Annu Rev Biochem 74:867-900
-
(2005)
Annu Rev Biochem
, vol.74
, pp. 867-900
-
-
Orengo, C.A.1
Thornton, J.M.2
-
137
-
-
33845545435
-
The modular nature of genetic diseases
-
Oti M, Brunner HG (2007) The modular nature of genetic diseases. Clin Genet 71:1-11
-
(2007)
Clin Genet
, vol.71
, pp. 1-11
-
-
Oti, M.1
Brunner, H.G.2
-
138
-
-
0033301555
-
Use of contiguity on the chromosome to predict functional coupling
-
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N (1999) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol 1:93-108
-
(1999)
Silico Biol
, vol.1
, pp. 93-108
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
139
-
-
33646380337
-
Adatabase and tool, IMBrowser, for exploring and integrating emerging gene and protein interaction data for Drosophila
-
Pacifico S, Liu G, Guest S, Parrish JR, Fotouhi F, Finley RL Jr (2006) Adatabase and tool, IMBrowser, for exploring and integrating emerging gene and protein interaction data for Drosophila. BMC Bioinformatics 7:195
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 195
-
-
Pacifico, S.1
Liu, G.2
Guest, S.3
Parrish, J.R.4
Fotouhi, F.5
Finley, R.L.6
-
140
-
-
20144387067
-
The MIPS mammalian protein-protein interaction database
-
Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW, Ruepp A, Frishman D (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics 21:832-834
-
(2005)
Bioinformatics
, vol.21
, pp. 832-834
-
-
Pagel, P.1
Kovac, S.2
Oesterheld, M.3
Brauner, B.4
Dunger-Kaltenbach, I.5
Frishman, G.6
Montrone, C.7
Mark, P.8
Stumpflen, V.9
Mewes, H.W.10
Ruepp, A.11
Frishman, D.12
-
141
-
-
38549132879
-
DIMA 2.0 predicted and known domain interactions
-
Pagel P, Oesterheld M, Tovstukhina O, Strack N, Stumpflen V, Frishman D (2007) DIMA 2.0 predicted and known domain interactions. Nucleic Acids Res 36:D651-D655
-
(2007)
Nucleic Acids Res
, vol.36
, pp. D651-D655
-
-
Pagel, P.1
Oesterheld, M.2
Tovstukhina, O.3
Strack, N.4
Stumpflen, V.5
Frishman, D.6
-
142
-
-
9244239761
-
A domain interaction map based on phylogenetic profiling
-
Pagel P, Wong P, Frishman D (2004) A domain interaction map based on phylogenetic profiling. J Mol Biol 344:1331-1346
-
(2004)
J Mol Biol
, vol.344
, pp. 1331-1346
-
-
Pagel, P.1
Wong, P.2
Frishman, D.3
-
143
-
-
0343229549
-
Species-specificity of the cohesin-dockerin interaction between Clostridium thermocellum and Clostridium cellulolyticum: Prediction of specificity determinants of the dockerin domain
-
Pages S, Belaich A, Belaich JP, Morag E, Lamed R, Shoham Y, Bayer EA (1997) Species-specificity of the cohesin-dockerin interaction between Clostridium thermocellum and Clostridium cellulolyticum: prediction of specificity determinants of the dockerin domain. Proteins 29:517-527
-
(1997)
Proteins
, vol.29
, pp. 517-527
-
-
Pages, S.1
Belaich, A.2
Belaich, J.P.3
Morag, E.4
Lamed, R.5
Shoham, Y.6
Bayer, E.A.7
-
144
-
-
33746156959
-
Global mapping of pharmacological space
-
Paolini GV, Shapland RH, Van Hoorn WP, Mason JS, Hopkins AL (2006) Global mapping of pharmacological space. Nat Biotechnol 24:805-815
-
(2006)
Nat Biotechnol
, vol.24
, pp. 805-815
-
-
Paolini, G.V.1
Shapland, R.H.2
Van Hoorn, W.P.3
Mason, J.S.4
Hopkins, A.L.5
-
145
-
-
0035970298
-
Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast
-
Park J, Lappe M, Teichmann SA (2001) Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol 307:929-938
-
(2001)
J Mol Biol
, vol.307
, pp. 929-938
-
-
Park, J.1
Lappe, M.2
Teichmann, S.A.3
-
146
-
-
38549161592
-
A proteome-wide protein interaction map for Campylobacter jejuni
-
Parrish JR, Yu J, Liu G, Hines JA, Chan JE, Mangiola BA, Zhang H, Pacifico S, Fotouhi F, Dirita VJ, Ideker T, Andrews P, Finley RL Jr (2007) A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol 8:R130
-
(2007)
Genome Biol
, vol.8
, pp. R130
-
-
Parrish, J.R.1
Yu, J.2
Liu, G.3
Hines, J.A.4
Chan, J.E.5
Mangiola, B.A.6
Zhang, H.7
Pacifico, S.8
Fotouhi, F.9
Dirita, V.J.10
Ideker, T.11
Andrews, P.12
Finley, R.L.13
-
147
-
-
22344437983
-
Identification of genomic features using microsyntenies of domains: Domain teams
-
Pasek S, Bergeron A, Risler JL, Louis A, Ollivier E, Raffinot M (2005) Identification of genomic features using microsyntenies of domains: domain teams. Genome Res 15:867-874
-
(2005)
Genome Res
, vol.15
, pp. 867-874
-
-
Pasek, S.1
Bergeron, A.2
Risler, J.L.3
Louis, A.4
Ollivier, E.5
Raffinot, M.6
-
148
-
-
0037453510
-
Assembly of cell regulatory systems through protein interaction domains
-
Pawson T, Nash P (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300:445-52
-
(2003)
Science
, vol.300
, pp. 445-452
-
-
Pawson, T.1
Nash, P.2
-
149
-
-
24644502565
-
Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome
-
Pazos F, Ranea JA, Juan D, Sternberg MJ (2005) Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J Mol Biol 352:1002-1015
-
(2005)
J Mol Biol
, vol.352
, pp. 1002-1015
-
-
Pazos, F.1
Ranea, J.A.2
Juan, D.3
Sternberg, M.J.4
-
150
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of protein-protein interaction
-
Pazos F, Valencia A (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 14:609-614
-
(2001)
Protein Eng
, vol.14
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
151
-
-
0001797110
-
Rapid generation of high quality approximate 2-dimension molecular structures
-
Pearlman RS (1987) Rapid generation of high quality approximate 2-dimension molecular structures. Chem Des Auto News 2:1-6
-
(1987)
Chem des Auto News
, vol.2
, pp. 1-6
-
-
Pearlman, R.S.1
-
152
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 96:4285-4288
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
153
-
-
35349024501
-
Network modeling links breast cancer susceptibility and centrosome dysfunction
-
Pujana MA, Han JD, Starita LM, Stevens KN, Tewari M, Ahn JS, Rennert G, Moreno V, Kirchhoff T, Gold B, Assmann V, Elshamy WM, Rual JF, Levine D, Rozek LS, Gelman RS, Gunsalus KC, Greenberg RA, Sobhian B, Bertin N, Venkatesan K, Ayivi-Guedehoussou N, Sole X, Hernandez P, Lazaro C, Nathanson KL, Weber BL, Cusick ME, Hill DE, Offit K, Livingston DM, Gruber SB, Parvin JD, Vidal M (2007) Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 39:1338-1349
-
(2007)
Nat Genet
, vol.39
, pp. 1338-1349
-
-
Pujana, M.A.1
Han, J.D.2
Starita, L.M.3
Stevens, K.N.4
Tewari, M.5
Ahn, J.S.6
Rennert, G.7
Moreno, V.8
Kirchhoff, T.9
Gold, B.10
Assmann, V.11
Elshamy, W.M.12
Rual, J.F.13
Levine, D.14
Rozek, L.S.15
Gelman, R.S.16
Gunsalus, K.C.17
Greenberg, R.A.18
Sobhian, B.19
Bertin, N.20
Venkatesan, K.21
Ayivi-Guedehoussou, N.22
Sole, X.23
Hernandez, P.24
Lazaro, C.25
Nathanson, K.L.26
Weber, B.L.27
Cusick, M.E.28
Hill, D.E.29
Offit, K.30
Livingston, D.M.31
Gruber, S.B.32
Parvin, J.D.33
Vidal, M.34
more..
-
154
-
-
0042622252
-
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
-
Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferre F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Kuster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ (2003) ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 31:3625-3630
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3625-3630
-
-
Puntervoll, P.1
Linding, R.2
Gemund, C.3
Chabanis-Davidson, S.4
Mattingsdal, M.5
Cameron, S.6
Martin, D.M.7
Ausiello, G.8
Brannetti, B.9
Costantini, A.10
Ferre, F.11
Maselli, V.12
Via, A.13
Cesareni, G.14
Diella, F.15
Superti-Furga, G.16
Wyrwicz, L.17
Ramu, C.18
McGuigan, C.19
Gudavalli, R.20
Letunic, I.21
Bork, P.22
Rychlewski, L.23
Kuster, B.24
Helmer-Citterich, M.25
Hunter, W.N.26
Aasland, R.27
Gibson, T.J.28
more..
-
156
-
-
12344317072
-
An integrative approach to gain insights into the cellular function of human ataxin-2
-
Ralser M, Albrecht M, Nonhoff U, Lengauer T, Lehrach H, Krobitsch S (2005) An integrative approach to gain insights into the cellular function of human ataxin-2. J Mol Biol 346:203-214
-
(2005)
J Mol Biol
, vol.346
, pp. 203-214
-
-
Ralser, M.1
Albrecht, M.2
Nonhoff, U.3
Lengauer, T.4
Lehrach, H.5
Krobitsch, S.6
-
157
-
-
34547858473
-
Computational analysis of human protein interaction networks
-
Ramirez F, Schlicker A, Assenov Y, Lengauer T, Albrecht M (2007) Computational analysis of human protein interaction networks. Proteomics 7:2541-2552
-
(2007)
Proteomics
, vol.7
, pp. 2541-2552
-
-
Ramirez, F.1
Schlicker, A.2
Assenov, Y.3
Lengauer, T.4
Albrecht, M.5
-
158
-
-
34447319220
-
Docking and scoring for structure-based drug design
-
Lengauer T ed, Wiley-VCH, Weinheim
-
Rarey M, Degen J, Reulecke I (2007) Docking and scoring for structure-based drug design. In: Lengauer T (ed) Bioinformatics - from genomes to therapies. Wiley-VCH, Weinheim, pp 541-600
-
(2007)
Bioinformatics - From Genomes to Therapies
, pp. 541-600
-
-
Rarey, M.1
Degen, J.2
Reulecke, I.3
-
159
-
-
0032149905
-
Feature trees: A new molecular similarity measure based on tree matching
-
Rarey M, Dixon JS (1998) Feature trees: a new molecular similarity measure based on tree matching. J Comput Aided Mol Des 12:471-490
-
(1998)
J Comput Aided Mol des
, vol.12
, pp. 471-490
-
-
Rarey, M.1
Dixon, J.S.2
-
160
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-489
-
(1996)
J Mol Biol
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
161
-
-
0032828715
-
A generic protein purification method for protein complex characterization and proteome exploration
-
Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17:1030-1032
-
(1999)
Nat Biotechnol
, vol.17
, pp. 1030-1032
-
-
Rigaut, G.1
Shevchenko, A.2
Rutz, B.3
Wilm, M.4
Mann, M.5
Seraphin, B.6
-
162
-
-
34548084807
-
Inferring protein domain interactions from databases of interacting proteins
-
Riley R, Lee C, Sabatti C, Eisenberg D (2005) Inferring protein domain interactions from databases of interacting proteins. Genome Biol 6:R89
-
(2005)
Genome Biol
, vol.6
, pp. R89
-
-
Riley, R.1
Lee, C.2
Sabatti, C.3
Eisenberg, D.4
-
163
-
-
38549163153
-
CORUM: The comprehensive resource of mammalian protein complexes
-
Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stumpflen V, Mewes HW (2008) CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res 36:D646-D650
-
(2008)
Nucleic Acids Res
, vol.36
, pp. D646-D650
-
-
Ruepp, A.1
Brauner, B.2
Dunger-Kaltenbach, I.3
Frishman, G.4
Montrone, C.5
Stransky, M.6
Waegele, B.7
Schmidt, T.8
Doudieu, O.N.9
Stumpflen, V.10
Mewes, H.W.11
-
164
-
-
34548394483
-
Human protein-protein interaction networks and the value for drug discovery
-
Ruffner H, Bauer A, Bouwmeester T (2007) Human protein-protein interaction networks and the value for drug discovery. Drug Discov Today 12:709-716
-
(2007)
Drug Discov Today
, vol.12
, pp. 709-716
-
-
Ruffner, H.1
Bauer, A.2
Bouwmeester, T.3
-
165
-
-
0028466540
-
Comparison of automatic three-dimensional models builders using 639 X-ray structures
-
Sadowski J, Gasteiger J, Klebe G (1994) Comparison of automatic three-dimensional models builders using 639 X-ray structures. J Chem Inf Comput Sci 34:1000-1008
-
(1994)
J Chem Inf Comput Sci
, vol.34
, pp. 1000-1008
-
-
Sadowski, J.1
Gasteiger, J.2
Klebe, G.3
-
166
-
-
0036493195
-
Interaction generality, a measurement toassess the reliability of a protein-protein interaction
-
Saito R, Suzuki H, Hayashizaki Y (2002) Interaction generality, a measurement toassess the reliability of a protein-protein interaction. Nucleic Acids Res 30:1163-1168
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1163-1168
-
-
Saito, R.1
Suzuki, H.2
Hayashizaki, Y.3
-
167
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 32:D449-D451
-
(2004)
Nucleic Acids Res
, vol.32
, pp. D449-D451
-
-
Salwinski, L.1
Miller, C.S.2
Smith, A.J.3
Pettit, F.K.4
Bowie, J.U.5
Eisenberg, D.6
-
169
-
-
33749870873
-
Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions
-
Sato T, Yamanishi Y, Horimoto K, Kanehisa M, Toh H (2006) Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. Bioinformatics 22:2488-2492
-
(2006)
Bioinformatics
, vol.22
, pp. 2488-2492
-
-
Sato, T.1
Yamanishi, Y.2
Horimoto, K.3
Kanehisa, M.4
Toh, H.5
-
170
-
-
24144476642
-
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships
-
Sato T, Yamanishi Y, Kanehisa M, Toh H (2005) The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 21:3482-3489
-
(2005)
Bioinformatics
, vol.21
, pp. 3482-3489
-
-
Sato, T.1
Yamanishi, Y.2
Kanehisa, M.3
Toh, H.4
-
171
-
-
34248576303
-
Functional evaluation of domain-domain interactions and human protein interaction networks
-
Schlicker A, Huthmacher C, Ramirez F, Lengauer T, Albrecht M (2007) Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics 23:859-865
-
(2007)
Bioinformatics
, vol.23
, pp. 859-865
-
-
Schlicker, A.1
Huthmacher, C.2
Ramirez, F.3
Lengauer, T.4
Albrecht, M.5
-
172
-
-
34547743903
-
Reuse of structural domain-domain interactions in protein networks
-
Schuster-Bockler B, Bateman A (2007) Reuse of structural domain-domain interactions in protein networks. BMC Bioinformatics 8:259
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 259
-
-
Schuster-Bockler, B.1
Bateman, A.2
-
173
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
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
-
(2003)
Genome Res
, vol.13
, 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
-
174
-
-
13844314048
-
Conserved patterns of protein interaction in multiple species
-
Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T (2005) Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A 102:1974-1979
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 1974-1979
-
-
Sharan, R.1
Suthram, S.2
Kelley, R.M.3
Kuhn, T.4
McCuine, S.5
Uetz, P.6
Sittler, T.7
Karp, R.M.8
Ideker, T.9
-
176
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R (2006) Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 49:534-553
-
(2006)
J Med Chem
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
-
177
-
-
1542286745
-
Quantifying modularity in the evolution of biomolecular systems
-
Snel B, Huynen MA (2004) Quantifying modularity in the evolution of biomolecular systems. Genome Res 14:391-397
-
(2004)
Genome Res
, vol.14
, pp. 391-397
-
-
Snel, B.1
Huynen, M.A.2
-
178
-
-
33748276474
-
Protein-ligand docking: Current status and future challenges
-
Sousa SF, Fernandes PA, Ramos MJ (2006) Protein-ligand docking: Current status and future challenges. Proteins 65:15-26
-
(2006)
Proteins
, vol.65
, pp. 15-26
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
179
-
-
0142059836
-
Protein complexes and functional modules in molecular networks
-
Spirin V, Mirny LA (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 100:12123-12128
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 12123-12128
-
-
Spirin, V.1
Mirny, L.A.2
-
180
-
-
0035943340
-
Correlated sequence-signatures as markers of protein-protein interaction
-
Sprinzak E, Margalit H (2001) Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 311:681-692
-
(2001)
J Mol Biol
, vol.311
, pp. 681-692
-
-
Sprinzak, E.1
Margalit, H.2
-
181
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34:D535-D539
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D535-D539
-
-
Stark, C.1
Breitkreutz, B.J.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
182
-
-
13444257903
-
3did: Interacting protein domains of known three-dimensional structure
-
Stein A, Russell RB, Aloy P (2005) 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res 33:D413-D417
-
(2005)
Nucleic Acids Res
, vol.33
, pp. D413-D417
-
-
Stein, A.1
Russell, R.B.2
Aloy, P.3
-
183
-
-
33751395622
-
The value of high quality protein-protein interaction networks for systems biology
-
Stelzl U, Wanker EE (2006) The value of high quality protein-protein interaction networks for systems biology. Curr Opin Chem Biol 10:551-558
-
(2006)
Curr Opin Chem Biol
, vol.10
, pp. 551-558
-
-
Stelzl, U.1
Wanker, E.E.2
-
184
-
-
35748962289
-
Tools for visually exploring biological networks
-
Suderman M, Hallett M (2007) Tools for visually exploring biological networks. Bioinformatics 23:2651-2659
-
(2007)
Bioinformatics
, vol.23
, pp. 2651-2659
-
-
Suderman, M.1
Hallett, M.2
-
185
-
-
10744231500
-
Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-β signaling network
-
Tewari M, Hu PJ, Ahn JS, Ayivi-Guedehoussou N, Vidalain PO, Li S, Milstein S, Armstrong CM, Boxem M, Butler MD, Busiguina S, Rual JF, Ibarrola N, Chaklos ST, Bertin N, Vaglio P, Edgley ML, King KV, Albert PS, Vandenhaute J, Pandey A, Riddle DL, Ruvkun G, Vidal M (2004) Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-β signaling network. Mol Cell 13:469-482
-
(2004)
Mol Cell
, vol.13
, pp. 469-482
-
-
Tewari, M.1
Hu, P.J.2
Ahn, J.S.3
Ayivi-Guedehoussou, N.4
Vidalain, P.O.5
Li, S.6
Milstein, S.7
Armstrong, C.M.8
Boxem, M.9
Butler, M.D.10
Busiguina, S.11
Rual, J.F.12
Ibarrola, N.13
Chaklos, S.T.14
Bertin, N.15
Vaglio, P.16
Edgley, M.L.17
King, K.V.18
Albert, P.S.19
Vandenhaute, J.20
Pandey, A.21
Riddle, D.L.22
Ruvkun, G.23
Vidal, M.24
more..
-
186
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz P (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
-
187
-
-
30844443758
-
Herpesviral protein networks and their interaction with the human proteome
-
Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, Berger B, Rajagopala SV, Roupelieva M, Rose D, Fossum E, Haas J (2006) Herpesviral protein networks and their interaction with the human proteome. Science 311:239-242
-
(2006)
Science
, vol.311
, pp. 239-242
-
-
Uetz, P.1
Dong, Y.A.2
Zeretzke, C.3
Atzler, C.4
Baiker, A.5
Berger, B.6
Rajagopala, S.V.7
Roupelieva, M.8
Rose, D.9
Fossum, E.10
Haas, J.11
-
189
-
-
34250191844
-
Reactome: A knowledge base of biologic pathways and processes
-
Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, De Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol 8:R39
-
(2007)
Genome Biol
, vol.8
, pp. R39
-
-
Vastrik, I.1
D'Eustachio, P.2
Schmidt, E.3
Joshi-Tope, G.4
Gopinath, G.5
Croft, D.6
De Bono, B.7
Gillespie, M.8
Jassal, B.9
Lewis, S.10
Matthews, L.11
Wu, G.12
Birney, E.13
Stein, L.14
-
190
-
-
1842861592
-
Structure, function and evolution of multidomain proteins
-
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
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 208-216
-
-
Vogel, C.1
Bashton, M.2
Kerrison, N.D.3
Chothia, C.4
Teichmann, S.A.5
-
191
-
-
35148862429
-
Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome
-
Von Brunn A, Teepe C, Simpson JC, Pepperkok R, Friedel CC, Zimmer R, Roberts R, Baric R, Haas J (2007) Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS ONE 2:e459
-
(2007)
PLoS ONE
, vol.2
, pp. e459
-
-
Von Brunn, A.1
Teepe, C.2
Simpson, J.C.3
Pepperkok, R.4
Friedel, C.C.5
Zimmer, R.6
Roberts, R.7
Baric, R.8
Haas, J.9
-
192
-
-
33846086800
-
STRING 7 - Recent developments in the integration and prediction of protein interactions
-
Von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P (2007) STRING 7 - recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35:D358-D362
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D358-D362
-
-
Von Mering, C.1
Jensen, L.J.2
Kuhn, M.3
Chaffron, S.4
Doerks, T.5
Kruger, B.6
Snel, B.7
Bork, P.8
-
193
-
-
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
-
(2002)
Nature
, vol.417
, 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
-
194
-
-
41849115573
-
InSite: A computational method for identifying protein-protein interaction binding sites on a proteome-wide scale
-
Wang H, Segal E, Ben-Hur A, Li QR, Vidal M, Koller D (2007a) InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. Genome Biol 8:R192
-
(2007)
Genome Biol
, vol.8
, pp. R192
-
-
Wang, H.1
Segal, E.2
Ben-Hur, A.3
Li, Q.R.4
Vidal, M.5
Koller, D.6
-
195
-
-
0037763817
-
Comparative evaluation of 11 scoring functions for molecular docking
-
Wang R, Lu Y, Wang S (2003) Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 46:2287-2303
-
(2003)
J Med Chem
, vol.46
, pp. 2287-2303
-
-
Wang, R.1
Lu, Y.2
Wang, S.3
-
196
-
-
38849149616
-
Analysis on multi-domain cooperation for predicting protein-protein interactions
-
Wang RS, Wang Y, Wu LY, Zhang XS, Chen L (2007b) Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformatics 8:391
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 391
-
-
Wang, R.S.1
Wang, Y.2
Wu, L.Y.3
Zhang, X.S.4
Chen, L.5
-
197
-
-
0023965741
-
SMILES, a chemical language and information system. 1. Introduction and encoding rules
-
Weininger D (1988) SMILES, a chemical language and information system. 1. Introduction and encoding rules. J Chem Inf Comput Sci 28:31-36
-
(1988)
J Chem Inf Comput Sci
, vol.28
, pp. 31-36
-
-
Weininger, D.1
-
198
-
-
37249004920
-
Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
-
Wells JA, McClendon CL (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450:1001-1009
-
(2007)
Nature
, vol.450
, pp. 1001-1009
-
-
Wells, J.A.1
McClendon, C.L.2
-
199
-
-
33846062023
-
Database resources of the national center for biotechnology information
-
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Di Cuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 35:D5-D12
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D5-D12
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
Di Cuccio, M.8
Edgar, R.9
Federhen, S.10
Geer, L.Y.11
Kapustin, Y.12
Khovayko, O.13
Landsman, D.14
Lipman, D.J.15
Madden, T.L.16
Maglott, D.R.17
Ostell, J.18
Miller, V.19
Pruitt, K.D.20
Schuler, G.D.21
Sequeira, E.22
Sherry, S.T.23
Sirotkin, K.24
Souvorov, A.25
Starchenko, G.26
Tatusov, R.L.27
Tatusova, T.A.28
Wagner, L.29
Yaschenko, E.30
more..
-
200
-
-
0033529707
-
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis
-
Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M'Rabet N, Menard P, Mittmann M, Pai C, Rebischung C, Revuelta JL, Riles L, Roberts CJ, Ross-MacDonald P, Scherens B, Snyder M, Sookhai-Mahadeo S, Storms RK, Veronneau S, Voet M, Volckaert G, Ward TR, Wysocki R, Yen GS, Yu K, Zimmermann K, Philippsen P, Johnston M, Davis RW (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906
-
(1999)
Science
, vol.285
, pp. 901-906
-
-
Winzeler, E.A.1
Shoemaker, D.D.2
Astromoff, A.3
Liang, H.4
Anderson, K.5
Andre, B.6
Bangham, R.7
Benito, R.8
Boeke, J.D.9
Bussey, H.10
Chu, A.M.11
Connelly, C.12
Davis, K.13
Dietrich, F.14
Dow, S.W.15
El Bakkoury, M.16
Foury, F.17
Friend, S.H.18
Gentalen, E.19
Giaever, G.20
Hegemann, J.H.21
Jones, T.22
Laub, M.23
Liao, H.24
Liebundguth, N.25
Lockhart, D.J.26
Lucau-Danila, A.27
Lussier, M.28
M'Rabet, N.29
Menard, P.30
Mittmann, M.31
Pai, C.32
Rebischung, C.33
Revuelta, J.L.34
Riles, L.35
Roberts, C.J.36
Ross-Mac Donald, P.37
Scherens, B.38
Snyder, M.39
Sookhai-Mahadeo, S.40
Storms, R.K.41
Veronneau, S.42
Voet, M.43
Volckaert, G.44
Ward, T.R.45
Wysocki, R.46
Yen, G.S.47
Yu, K.48
Zimmermann, K.49
Philippsen, P.50
Johnston, M.51
Davis, R.W.52
more..
-
201
-
-
0035224503
-
Protein-protein interaction map inference using interacting domain profile pairs
-
Wojcik J, Schachter V (2001) Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics 17(Suppl 1):S296-S305
-
(2001)
Bioinformatics
, vol.17
, pp. S296-S305
-
-
Wojcik, J.1
Schachter, V.2
-
202
-
-
3943087720
-
Analyzing cellular biochemistry in terms of molecular networks
-
Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M (2004) Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem 73:1051-1087
-
(2004)
Annu Rev Biochem
, vol.73
, pp. 1051-1087
-
-
Xia, Y.1
Yu, H.2
Jansen, R.3
Seringhaus, M.4
Baxter, S.5
Greenbaum, D.6
Zhao, H.7
Gerstein, M.8
-
203
-
-
33751017706
-
Discovering disease-genes by topological features in human protein-protein interaction network
-
Xu J, Li Y (2006) Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics 22:2800-2805
-
(2006)
Bioinformatics
, vol.22
, pp. 2800-2805
-
-
Xu, J.1
Li, Y.2
-
204
-
-
36849004497
-
A modular network model of aging
-
Xue H, Xian B, Dong D, Xia K, Zhu S, Zhang Z, Hou L, Zhang Q, Zhang Y, Han JD (2007) A modular network model of aging. Mol Syst Biol 3:147
-
(2007)
Mol Syst Biol
, vol.3
, pp. 147
-
-
Xue, H.1
Xian, B.2
Dong, D.3
Xia, K.4
Zhu, S.5
Zhang, Z.6
Hou, L.7
Zhang, Q.8
Zhang, Y.9
Han, J.D.10
-
205
-
-
0034265657
-
Evaluation of descriptors and mini-fingerprints for the identification of molecules with similar activity
-
Xue L, Godden JW, Bajorath J (2000) Evaluation of descriptors and mini-fingerprints for the identification of molecules with similar activity. J Chem Inf Comput Sci 40:1227-1234
-
(2000)
J Chem Inf Comput Sci
, vol.40
, pp. 1227-1234
-
-
Xue, L.1
Godden, J.W.2
Bajorath, J.3
-
206
-
-
33745957790
-
"Bits" and pieces
-
Yaffe MB (2006) "Bits" and pieces. Sci STKE 2006:pe28
-
(2006)
Sci STKE
, vol.2006
, pp. pe28
-
-
Yaffe, M.B.1
-
207
-
-
35148838537
-
Drug-target network
-
Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M (2007) Drug-target network. Nat Biotechnol 25:1119-1126
-
(2007)
Nat Biotechnol
, vol.25
, pp. 1119-1126
-
-
Yildirim, M.A.1
Goh, K.I.2
Cusick, M.E.3
Barabasi, A.L.4
Vidal, M.5
-
208
-
-
1842580761
-
Functional and topological characterization of protein interaction networks
-
Yook SH, Oltvai ZN, Barabasi AL (2004) Functional and topological characterization of protein interaction networks. Proteomics 4:928-942
-
(2004)
Proteomics
, vol.4
, pp. 928-942
-
-
Yook, S.H.1
Oltvai, Z.N.2
Barabasi, A.L.3
-
209
-
-
34247622363
-
The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics
-
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
-
(2007)
PLoS Comput Biol
, vol.3
, pp. e59
-
-
Yu, H.1
Kim, P.M.2
Sprecher, E.3
Trifonov, V.4
Gerstein, M.5
-
210
-
-
0013033597
-
The structure and function of proline recognition domains
-
Zarrinpar A, Bhattacharyya RP, Lim WA (2003) The structure and function of proline recognition domains. Sci STKE 2003: RE8
-
(2003)
Sci STKE
, vol.2003
, pp. RE8
-
-
Zarrinpar, A.1
Bhattacharyya, R.P.2
Lim, W.A.3
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