-
1
-
-
0037093640
-
-
Janin J. Welcome to CAPRI; a critical assessment of predicted interactions. Proteins 2002;47:257.
-
Janin J. Welcome to CAPRI; a critical assessment of predicted interactions. Proteins 2002;47:257.
-
-
-
-
2
-
-
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
-
3
-
-
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
-
4
-
-
0038583687
-
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
-
Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003;12:1271-1282.
-
(2003)
Protein Sci
, vol.12
, pp. 1271-1282
-
-
Zacharias, M.1
-
5
-
-
21644435306
-
ATTRACT: Protein-protein docking in CAPRI using a reduced protein model
-
Zacharias M. ATTRACT: protein-protein docking in CAPRI using a reduced protein model. Proteins 2005;60:252-256.
-
(2005)
Proteins
, vol.60
, pp. 252-256
-
-
Zacharias, M.1
-
6
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith GR, Sternberg MJE. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.E.2
-
7
-
-
1542316339
-
Rapid Protein-ligand docking including soft degrees of freedom from molecular dynamics simulations to account for protein flexibility: FK506 binding to FKBP binding protein as an example
-
Zacharias M. Rapid Protein-ligand docking including soft degrees of freedom from molecular dynamics simulations to account for protein flexibility: FK506 binding to FKBP binding protein as an example. Proteins 2004;54:759-767.
-
(2004)
Proteins
, vol.54
, pp. 759-767
-
-
Zacharias, M.1
-
8
-
-
29144485503
-
Accounting for protein deformability during protein-protein and protein-ligand docking
-
May A, Zacharias M. Accounting for protein deformability during protein-protein and protein-ligand docking. Biochim Biophys Acta 2005;1754:225-231.
-
(2005)
Biochim Biophys Acta
, vol.1754
, pp. 225-231
-
-
May, A.1
Zacharias, M.2
-
10
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter atomic analysis
-
Tirion MM. Large amplitude elastic motions in proteins from a single-parameter atomic analysis. Phys Rev Lett 1996;77:1905-1908.
-
(1996)
Phys Rev Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
11
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997;2:173-181.
-
(1997)
Fold Des
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
12
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998;33:417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
13
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama F, Sanejouand YH. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001;14:1-6.
-
(2001)
Protein Eng
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
14
-
-
30044434744
-
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
-
Tobi D, Bahar I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci USA 2005;102:18908-18913.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 18908-18913
-
-
Tobi, D.1
Bahar, I.2
-
15
-
-
25844431698
-
Coarse-grained normal mode analysis in structural biology
-
Bahar I, Rader EJ. Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 2005;15:586-592.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 586-592
-
-
Bahar, I.1
Rader, E.J.2
-
16
-
-
23344454719
-
Refinement of docked protein-ligand and protein-DNA structures using low-frequency normal mode amplitude optimization
-
Lindahl E, Delarue M. Refinement of docked protein-ligand and protein-DNA structures using low-frequency normal mode amplitude optimization. Nucleic Acids Res 2005;33:4496-4506.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4496-4506
-
-
Lindahl, E.1
Delarue, M.2
-
17
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
-
Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
18
-
-
36749036564
-
-
Case D, Pearlman DA, Caldwell JW, Cheatham III, TE, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA. Amber 8. University of California, 2003, San Francisco.
-
Case D, Pearlman DA, Caldwell JW, Cheatham III, TE, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA. Amber 8. University of California, 2003, San Francisco.
-
-
-
-
19
-
-
0032840382
-
Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger peptidyl-tRNA hydrolysis
-
Frolova LY, Tsivkovskii RY, Sivolobova GF, Oparina NY, Serpinsky OI, Blinov VM, Tatkov SI, Kisselev LL. Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger peptidyl-tRNA hydrolysis. RNA 1999;5:1014-1020.
-
(1999)
RNA
, vol.5
, pp. 1014-1020
-
-
Frolova, L.Y.1
Tsivkovskii, R.Y.2
Sivolobova, G.F.3
Oparina, N.Y.4
Serpinsky, O.I.5
Blinov, V.M.6
Tatkov, S.I.7
Kisselev, L.L.8
-
20
-
-
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. Mol Cell 2005;20:917-927.
-
(2005)
Mol 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
-
22
-
-
33644843079
-
Accounting for loop flexibility during protein-protein docking
-
Bastard K, Prevost C, Zacharias M. Accounting for loop flexibility during protein-protein docking. Proteins 2006;62:956-969.
-
(2006)
Proteins
, vol.62
, pp. 956-969
-
-
Bastard, K.1
Prevost, C.2
Zacharias, M.3
-
23
-
-
20844445832
-
Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing
-
Hou Z, Bernstein D, 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.2
Fox, C.A.3
Keck, J.L.4
-
24
-
-
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
-
25
-
-
0032944877
-
A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with Orc1 protein in Saccharomyces cerevisiae
-
Gardner KA, Rine J, Fox CA. A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with Orc1 protein in Saccharomyces cerevisiae. Genetics 1999;151:31-44.
-
(1999)
Genetics
, vol.151
, pp. 31-44
-
-
Gardner, K.A.1
Rine, J.2
Fox, C.A.3
-
26
-
-
34247473840
-
Molecular mimicry enables competitive recruitment by natively disordered protein
-
Bonsor DA, Grishkovskaya I, Dodson EJ, Kleanthous C. Molecular mimicry enables competitive recruitment by 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
-
27
-
-
34548726434
-
Novel and unexpected complex between the SUMO-1-conjugating enzyme UBC9 and the ubiquitin-conjugating enzyme E2-25 kDa
-
in press
-
Walker JR, Awakumov GV, Xue S, Newman EM, Mackenzie F, Weigelt J, Sundstrom M, Arrowsmith CH, Edwards AM, Bochkarev A, Dhe-Paganon SA. Novel and unexpected complex between the SUMO-1-conjugating enzyme UBC9 and the ubiquitin-conjugating enzyme E2-25 kDa, in press.
-
-
-
Walker, J.R.1
Awakumov, 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.A.11
-
28
-
-
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
-
29
-
-
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
-
30
-
-
1242342946
-
Deletion analyses of the peptidoglycan-associated lipoprotein Pal reveals three independent binding sequences including a TolA box
-
Cascales E, Lloubes R. Deletion analyses of the peptidoglycan-associated lipoprotein Pal reveals three independent binding sequences including a TolA box. Mol Microbiol 2004;51:873-885.
-
(2004)
Mol Microbiol
, vol.51
, pp. 873-885
-
-
Cascales, E.1
Lloubes, R.2
-
31
-
-
17844401751
-
SUMO modification of the ubiquitin-conjugating enzyme E2-25K
-
Pichler A, Knipscheer P, Oberhofer E, van Dijk WJ, Korner R, Velgaard Olsen J, Jentsch S, Melchior F, Sixma TK. SUMO modification of the ubiquitin-conjugating enzyme E2-25K. Nat Struct Biol 2005;12:264-269.
-
(2005)
Nat Struct Biol
, vol.12
, pp. 264-269
-
-
Pichler, A.1
Knipscheer, P.2
Oberhofer, E.3
van Dijk, W.J.4
Korner, R.5
Velgaard Olsen, J.6
Jentsch, S.7
Melchior, F.8
Sixma, T.K.9
-
32
-
-
33846227108
-
Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential
-
Kannan S, Zacharias M. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential. Proteins 2007;66:697-706.
-
(2007)
Proteins
, vol.66
, pp. 697-706
-
-
Kannan, S.1
Zacharias, M.2
-
33
-
-
26444587477
-
Refinement of protein cores and protein-peptide interfaces using a potential scaling approach
-
Riemann N, Zacharias M. Refinement of protein cores and protein-peptide interfaces using a potential scaling approach. Protein Eng 2005;18:465-476.
-
(2005)
Protein Eng
, vol.18
, pp. 465-476
-
-
Riemann, N.1
Zacharias, M.2
|