-
1
-
-
0033757806
-
The protein data bank and the challenge of structural genomics
-
Berman HM, Bhat TN, Bourne PE, Feng Z, Gilliland G, Weissig H, Westbrook J. The protein data bank and the challenge of structural genomics. Nat Struct Biol 2000;7(Suppl.):957-959.
-
(2000)
Nat Struct Biol
, vol.7
, Issue.SUPPL.
, pp. 957-959
-
-
Berman, H.M.1
Bhat, T.N.2
Bourne, P.E.3
Feng, Z.4
Gilliland, G.5
Weissig, H.6
Westbrook, J.7
-
2
-
-
1242270553
-
Protein-protein docking: Is the glass half-full or half-empty?
-
Vajda S, Camacho CJ. Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol 2004;22:110-116.
-
(2004)
Trends Biotechnol
, vol.22
, pp. 110-116
-
-
Vajda, S.1
Camacho, C.J.2
-
4
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
5
-
-
0038359614
-
CAPRI: A Critical Assessment of PRedicted Interactions
-
Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins 2003;52:2-9.
-
(2003)
Proteins
, vol.52
, pp. 2-9
-
-
Janin, J.1
Henrick, K.2
Moult, J.3
Eyck, L.T.4
Sternberg, M.J.5
Vajda, S.6
Vakser, I.7
Wodak, S.J.8
-
6
-
-
21644487998
-
The targets of CAPRI rounds 3-5
-
Janin J. The targets of CAPRI rounds 3-5. Proteins 2005;60:170-175.
-
(2005)
Proteins
, vol.60
, pp. 170-175
-
-
Janin, J.1
-
7
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: Current status of docking methods
-
Mendez R, Leplae R, De Maria L, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003;52:51-67.
-
(2003)
Proteins
, vol.52
, pp. 51-67
-
-
Mendez, R.1
Leplae, R.2
De Maria, L.3
Wodak, S.J.4
-
8
-
-
21644469377
-
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
-
Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.
-
(2005)
Proteins
, vol.60
, pp. 150-169
-
-
Mendez, R.1
Leplae, R.2
Lensink, M.F.3
Wodak, S.J.4
-
9
-
-
1842861590
-
Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications
-
Wodak SJ, Mendez R. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004;14:242-249.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 242-249
-
-
Wodak, S.J.1
Mendez, R.2
-
10
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
-
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
-
(2003)
J Mol Biol
, vol.331
, pp. 281-299
-
-
Gray, J.J.1
Moughon, S.2
Wang, C.3
Schueler-Furman, O.4
Kuhlman, B.5
Rohl, C.A.6
Baker, D.7
-
11
-
-
17744364070
-
Improved side-chain modeling for protein-protein docking
-
Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci 2005;14:1328-1339.
-
(2005)
Protein Sci
, vol.14
, pp. 1328-1339
-
-
Wang, C.1
Schueler-Furman, O.2
Baker, D.3
-
12
-
-
0023430366
-
Monte Carlo-minimization approach to the multiple-minima problem in protein folding
-
Li Z, Scheraga HA. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 1987;84:6611-6615.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 6611-6615
-
-
Li, Z.1
Scheraga, H.A.2
-
13
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
14
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003;326:1239-1259.
-
(2003)
J Mol Biol
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
15
-
-
21644459373
-
Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility
-
Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005;60:187-194.
-
(2005)
Proteins
, vol.60
, pp. 187-194
-
-
Schueler-Furman, O.1
Wang, C.2
Baker, D.3
-
16
-
-
0037406075
-
Cyclic coordinate descent: A robotics algorithm for protein loop closure
-
Canutescu AA, Dunbrack RL, Jr. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003;12: 963-972.
-
(2003)
Protein Sci
, vol.12
, pp. 963-972
-
-
Canutescu, A.A.1
Dunbrack Jr., R.L.2
-
17
-
-
2442449534
-
Modeling structurally variable regions in homologous proteins with rosetta
-
Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins 2004;55:656-677.
-
(2004)
Proteins
, vol.55
, pp. 656-677
-
-
Rohl, C.A.1
Strauss, C.E.2
Chivian, D.3
Baker, D.4
-
18
-
-
33751118503
-
Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
-
Bradley P, Baker D. Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 2006;65:922-929.
-
(2006)
Proteins
, vol.65
, pp. 922-929
-
-
Bradley, P.1
Baker, D.2
-
19
-
-
0037084101
-
The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors
-
Heurgue-Hamard V, Champ S, Engstrom A, Ehrenberg M, Buckingham RH. The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J 2002;21:769-778.
-
(2002)
EMBO J
, vol.21
, pp. 769-778
-
-
Heurgue-Hamard, V.1
Champ, S.2
Engstrom, A.3
Ehrenberg, M.4
Buckingham, R.H.5
-
20
-
-
3042513877
-
Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase
-
Yang Z, Shipman L, Zhang M, Anton BP, Roberts RJ, Cheng X. Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase. J Mol Biol 2004;340:695-706.
-
(2004)
J Mol Biol
, vol.340
, pp. 695-706
-
-
Yang, Z.1
Shipman, L.2
Zhang, M.3
Anton, B.P.4
Roberts, R.J.5
Cheng, X.6
-
21
-
-
0038629269
-
Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase
-
Schubert HL, Phillips JD, Hill CP. Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase. Biochemistry 2003;42:5592-5599.
-
(2003)
Biochemistry
, vol.42
, pp. 5592-5599
-
-
Schubert, H.L.1
Phillips, J.D.2
Hill, C.P.3
-
22
-
-
0035697089
-
Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1
-
Vestergaard B, Van LB, Andersen GR, Nyborg J, Buckingham RH, Kjeldgaard M. Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1. Molecular cell 2001;8:1375-1382.
-
(2001)
Molecular cell
, vol.8
, pp. 1375-1382
-
-
Vestergaard, B.1
Van, L.B.2
Andersen, G.R.3
Nyborg, J.4
Buckingham, R.H.5
Kjeldgaard, M.6
-
23
-
-
29144491478
-
Molecular basis for bacterial class I release factor methylation by PrmC
-
Graille M, Heurgue-Hamard V, Champ S, Mora L, Scrima N, Ulryck N, van Tilbeurgh H, Buckingham RH. Molecular basis for bacterial class I release factor methylation by PrmC. Molecular cell 2005;20:917-927.
-
(2005)
Molecular cell
, vol.20
, pp. 917-927
-
-
Graille, M.1
Heurgue-Hamard, V.2
Champ, S.3
Mora, L.4
Scrima, N.5
Ulryck, N.6
van Tilbeurgh, H.7
Buckingham, R.H.8
-
24
-
-
34247244814
-
Structural basis for ARF1-mediated recruitment of ARHGAP21 to Golgi membranes
-
Menetrey J, Perderiset M, Cicolari J, Dubois T, Elkhatib N, El Khadali F, Franco M, Chavrier P, Houdusse A. Structural basis for ARF1-mediated recruitment of ARHGAP21 to Golgi membranes. EMBO J 2007;26:1953-1962.
-
(2007)
EMBO J
, vol.26
, pp. 1953-1962
-
-
Menetrey, J.1
Perderiset, M.2
Cicolari, J.3
Dubois, T.4
Elkhatib, N.5
El Khadali, F.6
Franco, M.7
Chavrier, P.8
Houdusse, A.9
-
25
-
-
34247473840
-
Molecular mimicry enables competitive recruitment by a natively disordered protein
-
Bonsor DA, Grishkovskaya I, Dodson EJ, Kleanthous C. Molecular mimicry enables competitive recruitment by a natively disordered protein. J Am Chem Soc 2007;129:4800-4807.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 4800-4807
-
-
Bonsor, D.A.1
Grishkovskaya, I.2
Dodson, E.J.3
Kleanthous, C.4
-
26
-
-
0037009519
-
Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing
-
Zhang Z, Hayashi MK, Merkel O, Stillman B, Xu RM. Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing. EMBO J 2002;21:4600-4611.
-
(2002)
EMBO J
, vol.21
, pp. 4600-4611
-
-
Zhang, Z.1
Hayashi, M.K.2
Merkel, O.3
Stillman, B.4
Xu, R.M.5
-
27
-
-
20844445832
-
Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing
-
Hou Z, Bernstein DA, Fox CA, Keck JL. Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc Natl Acad Sci USA 2005;102:8489-8494.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 8489-8494
-
-
Hou, Z.1
Bernstein, D.A.2
Fox, C.A.3
Keck, J.L.4
-
28
-
-
0346725950
-
The origin recognition complex and Sir4 protein recruit Sir1p to yeast silent chromatin through independent interactions requiring a common Sir1p domain
-
Bose ME, McConnell KH, Gardner-Aukema KA, Muller U, Weinreich M, Keck JL, Fox CA. The origin recognition complex and Sir4 protein recruit Sir1p to yeast silent chromatin through independent interactions requiring a common Sir1p domain. Mol Cell Biol 2004;24:774-786.
-
(2004)
Mol Cell Biol
, vol.24
, pp. 774-786
-
-
Bose, M.E.1
McConnell, K.H.2
Gardner-Aukema, K.A.3
Muller, U.4
Weinreich, M.5
Keck, J.L.6
Fox, C.A.7
-
29
-
-
0029096888
-
Structure of the binding site for inositol phosphates in a PH domain
-
Hyvonen M, Macias MJ, Nilges M, Oschkinat H, Saraste M, Wilmanns M. Structure of the binding site for inositol phosphates in a PH domain. The EMBO J 1995;14:4676-4685.
-
(1995)
The EMBO J
, vol.14
, pp. 4676-4685
-
-
Hyvonen, M.1
Macias, M.J.2
Nilges, M.3
Oschkinat, H.4
Saraste, M.5
Wilmanns, M.6
-
30
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
32
-
-
27944510194
-
Membrane recruitment of effector proteins by Arf and Rab GTPases
-
Kawasaki M, Nakayama K, Wakatsuki S. Membrane recruitment of effector proteins by Arf and Rab GTPases. Curr Opin Struct Biol 2005;15:681-689.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 681-689
-
-
Kawasaki, M.1
Nakayama, K.2
Wakatsuki, S.3
-
33
-
-
0034650563
-
The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9
-
Carr S, Penfold CN, Bamford V, James R, Hemmings AM. The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9. Structure 2000;8:57-66.
-
(2000)
Structure
, vol.8
, pp. 57-66
-
-
Carr, S.1
Penfold, C.N.2
Bamford, V.3
James, R.4
Hemmings, A.M.5
-
34
-
-
36749038768
-
MAD structure of the periplasmic domain of the E. coli pal protein
-
to be published
-
Abergel C, Walburger A, Bouveret E, Claverie JM. MAD structure of the periplasmic domain of the E. coli pal protein, to be published.
-
-
-
Abergel, C.1
Walburger, A.2
Bouveret, E.3
Claverie, J.M.4
-
35
-
-
0033966170
-
Identification by genetic suppression of Escherichia coli TolB residues important for TolB-Pal interaction
-
Ray MC, Germon P, Vianney A, Portalier R, Lazzaroni JC. Identification by genetic suppression of Escherichia coli TolB residues important for TolB-Pal interaction. J Bacteriol 2000;182:821-824.
-
(2000)
J Bacteriol
, vol.182
, pp. 821-824
-
-
Ray, M.C.1
Germon, P.2
Vianney, A.3
Portalier, R.4
Lazzaroni, J.C.5
-
36
-
-
0344631755
-
-
Bouveret E, Benedetti H, Rigal A, Loret E, Lazdunski C. In vitro characterization of peptidoglycan-associated lipoprotein (PAL)-peptidoglycan and PAL-TolB interactions. J Bacteriol 1999;181:6306-6311.
-
Bouveret E, Benedetti H, Rigal A, Loret E, Lazdunski C. In vitro characterization of peptidoglycan-associated lipoprotein (PAL)-peptidoglycan and PAL-TolB interactions. J Bacteriol 1999;181:6306-6311.
-
-
-
-
37
-
-
0031848939
-
TolB protein of Escherichia coli K-12 interacts with the outer membrane peptidoglycan-associated proteins Pal, Lpp and OmpA
-
Clavel T, Germon P, Vianney A, Portalier R, Lazzaroni JC. TolB protein of Escherichia coli K-12 interacts with the outer membrane peptidoglycan-associated proteins Pal, Lpp and OmpA. Mol Microbiol 1998;29:359-367.
-
(1998)
Mol Microbiol
, vol.29
, pp. 359-367
-
-
Clavel, T.1
Germon, P.2
Vianney, A.3
Portalier, R.4
Lazzaroni, J.C.5
-
38
-
-
36749013510
-
Structural Genomics Consortium (SGC). Ubiquitin-conjugating enzyme E2-25 kDa (Huntington interacting protein 2)
-
to be published
-
Avvakumov GV, Choe J, Newman EM, Mackenzie F, Kozieradzki I, Bochkarev A, Sundstrom M, Arrowsmith C, Edwards A, Dhe-paganon S, Structural Genomics Consortium (SGC). Ubiquitin-conjugating enzyme E2-25 kDa (Huntington interacting protein 2), to be published.
-
-
-
Avvakumov, G.V.1
Choe, J.2
Newman, E.M.3
Mackenzie, F.4
Kozieradzki, I.5
Bochkarev, A.6
Sundstrom, M.7
Arrowsmith, C.8
Edwards, A.9
Dhe-paganon, S.10
-
39
-
-
0030772385
-
Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system
-
Tong H, Hateboer G, Perrakis A, Bernards R, Sixma TK. Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system. J Biol Chem 1997;272: 21381-21387.
-
(1997)
J Biol Chem
, vol.272
, pp. 21381-21387
-
-
Tong, H.1
Hateboer, G.2
Perrakis, A.3
Bernards, R.4
Sixma, T.K.5
-
40
-
-
17844401751
-
SUMO modification of the ubiquitin-conjugating enzyme E2-25K
-
Pichler A, Knipscheer P, Oberhofer E, van Dijk WJ, Korner R, Olsen JV, Jentsch S, Melchior F, Sixma TK. SUMO modification of the ubiquitin-conjugating enzyme E2-25K. Nat Struct Mol Biol 2005;12:264-269.
-
(2005)
Nat Struct Mol Biol
, vol.12
, pp. 264-269
-
-
Pichler, A.1
Knipscheer, P.2
Oberhofer, E.3
van Dijk, W.J.4
Korner, R.5
Olsen, J.V.6
Jentsch, S.7
Melchior, F.8
Sixma, T.K.9
-
41
-
-
34548726434
-
A novel and unexpected complex between the SUMO-1-conjugating enzyme UBC9 and the Ubiquitin-conjugating enzyme E2-25 kDa
-
to be published
-
Walker JR, Avvakumov GV, Xue S, Newman EM, Mackenzie F, Weigelt J, Sundstrom M, Arrowsmith CH, Edwards AM, Bochkarev A, Dhe-Paganon S. A novel and unexpected complex between the SUMO-1-conjugating enzyme UBC9 and the Ubiquitin-conjugating enzyme E2-25 kDa, to be published.
-
-
-
Walker, J.R.1
Avvakumov, G.V.2
Xue, S.3
Newman, E.M.4
Mackenzie, F.5
Weigelt, J.6
Sundstrom, M.7
Arrowsmith, C.H.8
Edwards, A.M.9
Bochkarev, A.10
Dhe-Paganon, S.11
-
42
-
-
23044505285
-
Regulation of Smurf2 ubiquitin ligase activity by anchoring the E2 to the HECT domain
-
Ogunjimi AA, Briant DJ, Pece-Barbara N, Le Roy C, Di Guglielmo GM, Kavsak P, Rasmussen RK, Seet BT, Sicheri F, Wrana JL. Regulation of Smurf2 ubiquitin ligase activity by anchoring the E2 to the HECT domain. Mol Cell 2005;19:297-308.
-
(2005)
Mol Cell
, vol.19
, pp. 297-308
-
-
Ogunjimi, A.A.1
Briant, D.J.2
Pece-Barbara, N.3
Le Roy, C.4
Di Guglielmo, G.M.5
Kavsak, P.6
Rasmussen, R.K.7
Seet, B.T.8
Sicheri, F.9
Wrana, J.L.10
-
43
-
-
0037093643
-
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
-
Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-294.
-
(2002)
Proteins
, vol.47
, pp. 281-294
-
-
Chen, R.1
Weng, Z.2
|