-
1
-
-
0032530836
-
A database of macromolecular motions
-
Gerstein,M. and Krebs,W. (1998) A database of macromolecular motions. Nucleic Acids Res., 26, 4280-4290.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 4280-4290
-
-
Gerstein, M.1
Krebs, W.2
-
2
-
-
0037246863
-
MolMovDB: Analysis and visualization of conformational change and structural flexibility
-
Echols,N., Milburn,D. and Gerstein,M. (2003) MolMovDB: Analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res., 31, 478-482.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 478-482
-
-
Echols, N.1
Milburn, D.2
Gerstein, M.3
-
3
-
-
0031010107
-
The kinetics of protein-protein recognition
-
Janin,J. (1997) The kinetics of protein-protein recognition. Proteins 28, 153-161.
-
(1997)
Proteins
, vol.28
, pp. 153-161
-
-
Janin, J.1
-
4
-
-
0038359614
-
CAPRI: A critical assessment of predicted interactions
-
Janin,J., Henrick,K., Moult,J., Eyck,L.T., Sternberg,M.J.E., Vajda,S., Vakser,I. and Wodak,S.J. (2003) CAPRI: A critical assessment of predicted interactions. Proteins, 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.E.5
Vajda, S.6
Vakser, I.7
Wodak, S.J.8
-
5
-
-
1842861590
-
Predictions of protein-protein interactions: The CAPRI experiment, its evaluation and implications
-
Wodak,S.J. and Mendez,R. (2004) Predictions of protein-protein interactions: The CAPRI experiment, its evaluation and implications. Curr. Opin. Struct. Biol., 14, 242-249.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 242-249
-
-
Wodak, S.J.1
Mendez, R.2
-
6
-
-
0035957528
-
FlexE: Efficient molecular docking considering protein structure variations
-
Claussen,H., Buning,C., Rarey,M. and 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
-
7
-
-
1442351132
-
Protein flexibility in ligand docking and virtual screening to protein kinases
-
Cavasotto,C.N. and Abagyan,R.A. (2004) Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol., 337, 209-225.
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 209-225
-
-
Cavasotto, C.N.1
Abagyan, R.A.2
-
8
-
-
1542316339
-
Rapid protein-ligand docking using soft modes from Molecular Dynamics simulations to account for protein deformability: Binding of FK505 to FKBP
-
Zacharias,M. (2004) Rapid protein-ligand docking using soft modes from Molecular Dynamics simulations to account for protein deformability: binding of FK505 to FKBP. Proteins, 54, 759-767.
-
(2004)
Proteins
, vol.54
, pp. 759-767
-
-
Zacharias, M.1
-
9
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin,I., Ma,B., Wolfson,H.J. and Nussinov,R. (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins, 47, 409-443.
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.J.3
Nussinov, R.4
-
10
-
-
0006298689
-
Correlation of structure and function in enzyme action
-
Koshland,D. (1963) Correlation of structure and function in enzyme action. Science, 142, 1533-1541.
-
(1963)
Science
, vol.142
, pp. 1533-1541
-
-
Koshland, D.1
-
11
-
-
12344307441
-
Conformational changes observed in enzyme crystal structures upon substrate binding
-
Gutteridge,A. and Thornton,J. (2005) Conformational changes observed in enzyme crystal structures upon substrate binding. J. Mol. Biol., 346, 21-28.
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 21-28
-
-
Gutteridge, A.1
Thornton, J.2
-
12
-
-
0037666888
-
Implications of protein flexibility for drug discovery
-
Teague,S.J. (2003) Implications of protein flexibility for drug discovery. Nature Rev. Drug Discov., 2, 527-541.
-
(2003)
Nature Rev. Drug Discov.
, vol.2
, pp. 527-541
-
-
Teague, S.J.1
-
13
-
-
10744226366
-
Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation
-
Bradley,P., Chivian,D., Meiler,J., Misura,K.M.S., Rohl,C.A., Schief,W.R., Wedemeyer,W.J., Scheuler-Furman,O., Murphy,P., Schonbrun,J., Strauss,C.E.M. and Baker,D. (2003) Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation. Proteins, 53(Suppl. 6), 457-468.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 457-468
-
-
Bradley, P.1
Chivian, D.2
Meiler, J.3
Misura, K.M.S.4
Rohl, C.A.5
Schief, W.R.6
Wedemeyer, W.J.7
Scheuler-Furman, O.8
Murphy, P.9
Schonbrun, J.10
Strauss, C.E.M.11
Baker, D.12
-
14
-
-
1642464839
-
Protein structure prediction using Rosetta
-
Rohl,C.A., Strauss,C.E.M., Misura,K.M.S. and Baker,D. (2004) Protein structure prediction using Rosetta. Methods Enzymol., 383, 66-93.
-
(2004)
Methods Enzymol.
, vol.383
, pp. 66-93
-
-
Rohl, C.A.1
Strauss, C.E.M.2
Misura, K.M.S.3
Baker, D.4
-
15
-
-
0242299185
-
Touchstone: A unified approach to protein structure prediction
-
Skolnick,J., Zhang,Y., Arakaki,A.K., Kolinski,A., Boniecki,M., Szilagyi,A. and Kihara,D. (2003) Touchstone: A unified approach to protein structure prediction. Proteins, 53(Suppl. 6), 469-479.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 469-479
-
-
Skolnick, J.1
Zhang, Y.2
Arakaki, A.K.3
Kolinski, A.4
Boniecki, M.5
Szilagyi, A.6
Kihara, D.7
-
16
-
-
0035914481
-
Molecular dynamics in the endgame of protein structure prediction
-
Lee,M.R., Tsai,J., Baker,D. and Kollman,P.A. (2001) Molecular dynamics in the endgame of protein structure prediction. J. Mol. Biol., 313, 417-430.
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 417-430
-
-
Lee, M.R.1
Tsai, J.2
Baker, D.3
Kollman, P.A.4
-
17
-
-
0347481194
-
Application of statistical potentials to protein structure refinement from low resolution ab initio models
-
Lu,H. and Skolnick,J. (2003) Application of statistical potentials to protein structure refinement from low resolution ab initio models. Biopolymers, 70, 575-584.
-
(2003)
Biopolymers
, vol.70
, pp. 575-584
-
-
Lu, H.1
Skolnick, J.2
-
18
-
-
0347994106
-
Refinement of homology-based protein structures by molecular dynamics simulation techniques
-
Fan,H. and Mark,A. (2004) Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci. 13, 211-220.
-
(2004)
Protein Sci.
, vol.13
, pp. 211-220
-
-
Fan, H.1
Mark, A.2
-
19
-
-
20444374120
-
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling
-
Chen,J., Won,H.S., Im,W., Dyson,H.J. and Brooks,C.L.,III. (2005) Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J. Biomol. NMR, 31, 59-64.
-
(2005)
J. Biomol. NMR
, vol.31
, pp. 59-64
-
-
Chen, J.1
Won, H.S.2
Im, W.3
Dyson, H.J.4
Brooks III, C.L.5
-
20
-
-
0242267499
-
Assessment of progress over the CASP experiments
-
Venclovas,C., Zemla,A., Fidelis,K. and Moult,J. (2003) Assessment of progress over the CASP experiments. Proteins, 53(Suppl. 6), 585-595.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 585-595
-
-
Venclovas, C.1
Zemla, A.2
Fidelis, K.3
Moult, J.4
-
21
-
-
0242330730
-
Assessment of homology-based predictions in CASP5
-
Tramontano,A. and Morea,V. (2003) Assessment of homology-based predictions in CASP5. Proteins, 53(Suppl. 6), 352-368.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 352-368
-
-
Tramontano, A.1
Morea, V.2
-
22
-
-
13844267637
-
Determining the structure of an unliganded and fully glycosylated SIV gp120 envelope glycoprotein
-
Chen,B., Vogan,E.M., Gong,H., Skehel,J.J., Wiley,D.C. and Harrisson,S.C. (2005) Determining the structure of an unliganded and fully glycosylated SIV gp120 envelope glycoprotein. Structure, 13, 197-211.
-
(2005)
Structure
, vol.13
, pp. 197-211
-
-
Chen, B.1
Vogan, E.M.2
Gong, H.3
Skehel, J.J.4
Wiley, D.C.5
Harrisson, S.C.6
-
23
-
-
0344120716
-
Low-resolution structure refinement in electron microscopy
-
Chen,J.Z., Furst,J., Chapman,M.S. and Grigorieff,N. (2003) Low-resolution structure refinement in electron microscopy. J. Struct. Biol., 144, 144-151.
-
(2003)
J. Struct. Biol.
, vol.144
, pp. 144-151
-
-
Chen, J.Z.1
Furst, J.2
Chapman, M.S.3
Grigorieff, N.4
-
24
-
-
13844253945
-
Conformational changes of p97 during nucleotide hydrolysis determined by small-angle X-Ray scattering
-
Davies,J.M., Tsuruta,H., May,A.P. and Weis,W.I. (2005) Conformational changes of p97 during nucleotide hydrolysis determined by small-angle X-Ray scattering. Structure (Camb.), 13, 183-195.
-
(2005)
Structure (Camb.)
, vol.13
, pp. 183-195
-
-
Davies, J.M.1
Tsuruta, H.2
May, A.P.3
Weis, W.I.4
-
25
-
-
0026597444
-
Free R value: Novel statistical quantity for assessing the accuracy of crystal structures
-
Brünger,A.T. (1992) Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-475.
-
(1992)
Nature
, vol.355
, pp. 472-475
-
-
Brünger, A.T.1
-
26
-
-
0020771265
-
Dynamics of a small globular protein in terms of low-frequency vibrational modes
-
Go,N., Noguti,T. and Nishikawa,T. (1983) Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl Acad. Sci. USA, 80, 3696-3700.
-
(1983)
Proc. Natl. Acad. Sci. USA
, vol.80
, pp. 3696-3700
-
-
Go, N.1
Noguti, T.2
Nishikawa, T.3
-
27
-
-
0000991642
-
Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
-
Brooks,B.R. and Karplus,M. (1983) Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl Acad. Sci. USA, 80, 6571-6575.
-
(1983)
Proc. Natl. Acad. Sci. USA
, vol.80
, pp. 6571-6575
-
-
Brooks, B.R.1
Karplus, M.2
-
28
-
-
0022419152
-
Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
-
Levitt,M., Sander,C. and Stern,P.S. (1985) Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181, 423-447.
-
(1985)
J. Mol. Biol.
, vol.181
, pp. 423-447
-
-
Levitt, M.1
Sander, C.2
Stern, P.S.3
-
29
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion,M.M. (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett., 77, 1905-1908.
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
30
-
-
0036307741
-
The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus
-
Tama,F. and Brooks,C.L.,III (2002) The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J. Mol. Biol., 318, 733-747.
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 733-747
-
-
Tama, F.1
Brooks III, C.L.2
-
31
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
Tama,F., Valle,M., Frank,J. and Brooks,C.L.,III (2003) Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl Acad. Sci. USA 100, 9319-9323.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks III, C.L.4
-
32
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama,F. and Sanejouand,Y.-H. (2001)Conformational change of proteins arising from normal mode calculations. Protein Eng., 14, 1-6.
-
(2001)
Protein Eng.
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.-H.2
-
33
-
-
0036721233
-
Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
-
Krebs,W.G., Alexandrov,V., Wilson,C.A., Echols,N., Yu,H. and Gerstein,M. (2002) Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic. Proteins, 48, 682-695.
-
(2002)
Proteins
, vol.48
, pp. 682-695
-
-
Krebs, W.G.1
Alexandrov, V.2
Wilson, C.A.3
Echols, N.4
Yu, H.5
Gerstein, M.6
-
34
-
-
0030888546
-
Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation
-
Hayward,S., Kitao,A. and Berendsen,H.J.C. (1997) Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation. Proteins, 27, 425-437.
-
(1997)
Proteins
, vol.27
, pp. 425-437
-
-
Hayward, S.1
Kitao, A.2
Berendsen, H.J.C.3
-
35
-
-
2342518038
-
On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
-
Delarue,M. and Dumas,P. (2004) On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proc. Natl Acad. Sci. USA, 101, 6957-6962.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 6957-6962
-
-
Delarue, M.1
Dumas, P.2
-
36
-
-
3242883858
-
On the potential of normal-mode analysis for solving difficult molecular-replacement problems
-
Suhre,K. and Sanejouand,Y.-H. (2004) On the potential of normal-mode analysis for solving difficult molecular-replacement problems. Acta Crystallogr. D Biol. Crystallogr., 60, 796-799.
-
(2004)
Acta Crystallogr. D Biol. Crystallogr.
, vol.60
, pp. 796-799
-
-
Suhre, K.1
Sanejouand, Y.-H.2
-
37
-
-
4344716056
-
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
-
Tama,F., Miyashita,O. and Brooks,C.L.,III (2004) Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol., 147, 315-326.
-
(2004)
J. Struct. Biol.
, vol.147
, pp. 315-326
-
-
Tama, F.1
Miyashita, O.2
Brooks III, C.L.3
-
38
-
-
17044432465
-
Normal mode-based fitting of atomic structure into electron density maps: Application to sarcoplasmic reticulum Ca-ATPase
-
Hinsen,K., Navaza,J., Stokes,D.L. and Lacapere,J.J. (2005) Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. Biophys. J., 88, 818-827.
-
(2005)
Biophys. J.
, vol.88
, pp. 818-827
-
-
Hinsen, K.1
Navaza, J.2
Stokes, D.L.3
Lacapere, J.J.4
-
39
-
-
7444236378
-
Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation
-
Qian,B., Ortiz,A.R. and Baker,D. (2004) Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proc. Natl Acad. Sci. USA, 101 15346-15351.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 15346-15351
-
-
Qian, B.1
Ortiz, A.R.2
Baker, D.3
-
40
-
-
0001147249
-
Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex
-
Zacharias,M. and Sklenar,H. (1999) Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex. J. Comput. Chem., 20, 287-300.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 287-300
-
-
Zacharias, M.1
Sklenar, H.2
-
41
-
-
0021095856
-
Protein folding by restrained energy minimization and molecular dynamics
-
Levitt,M. (1983) Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol., 170, 723-764.
-
(1983)
J. Mol. Biol.
, vol.170
, pp. 723-764
-
-
Levitt, M.1
-
42
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen,K. (1998) Analysis of domain motions by approximate normal mode calculations. Proteins, 33, 417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
43
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Bahar,I., Atilgan,A.R. and Erman,B. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J., 80, 505-515.
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
44
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar,I., Atligan,A.R. and Erman,B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des., 2, 173-181.
-
(1997)
Fold. Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atligan, A.R.2
Erman, B.3
-
45
-
-
0036077875
-
Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model
-
Delarue,M. and Sanejouand,Y.-H. (2002) Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model. J. Mol. Biol., 320, 1011-1024.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 1011-1024
-
-
Delarue, M.1
Sanejouand, Y.-H.2
-
47
-
-
0028454915
-
A new approach for determining low-frequency normal modes in macromolecules
-
Durand,P., Trinquier,G. and Sanejouand,Y.-H. (1994) A new approach for determining low-frequency normal modes in macromolecules. Biopolymers 34, 759-771.
-
(1994)
Biopolymers
, vol.34
, pp. 759-771
-
-
Durand, P.1
Trinquier, G.2
Sanejouand, Y.-H.3
-
48
-
-
0034308140
-
Building-block approach for determining low-frequency normal modes of macromolecules
-
Tama,F., Gadea,F.X., Marques,O. and Sanejouand,Y.-H. (2000) Building-block approach for determining low-frequency normal modes of macromolecules. Proteins, 31, 1-7.
-
(2000)
Proteins
, vol.31
, pp. 1-7
-
-
Tama, F.1
Gadea, F.X.2
Marques, O.3
Sanejouand, Y.-H.4
-
49
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculation
-
Brooks,B.R., Bruccoleri,R.E., Olafson,B.D., States,D.J., Swaminathan,S. and Karplus,M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculation. J. Comput. Chem., 4, 187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
50
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg,D. and McLachlan,A.D. (1986) Solvation energy in protein folding and binding. Nature, 319, 199-203.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
51
-
-
0028063257
-
Polar and nonpolar atomic environments in the protein core: Implications for folding and binding
-
Koehl,P. and Delarue,M. (1994) Polar and nonpolar atomic environments in the protein core: Implications for folding and binding. Proteins, 20, 264-278.
-
(1994)
Proteins
, vol.20
, pp. 264-278
-
-
Koehl, P.1
Delarue, M.2
-
52
-
-
0000732463
-
A limited memory algorithm for bound constrained optimization
-
Byrd,R.H., Lu,P. and Nocedal,J. (1995) A limited memory algorithm for bound constrained optimization. SIAM J. Sci. Stat. Comput., 16 1190-1208.
-
(1995)
SIAM J. Sci. Stat. Comput.
, vol.16
, pp. 1190-1208
-
-
Byrd, R.H.1
Lu, P.2
Nocedal, J.3
-
53
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: The RESP model
-
Bayly,C.I., Cieplak,P., Cornell,W.D. and Kollman,P.A. (1993) A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: The RESP model. J. Phys. Chem., 97, 10269-10280.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
54
-
-
0036468385
-
Predictions of protein-protein interactions by docking methods
-
Smith,G.R. and Sternberg,M.J. (2002) Predictions of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol., 12 28-35.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.2
-
55
-
-
0036601150
-
Computational methods for the prediction of protein interactions
-
Valencia,A. and Pazos,F. (2002) Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol., 12, 368-373.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 368-373
-
-
Valencia, A.1
Pazos, F.2
-
56
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: Current status of docking methods
-
Mendez,R., Leplae,R., Maria,L. and Wodak,S.J. (2003) Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins, 52, 51-67.
-
(2003)
Proteins
, vol.52
, pp. 51-67
-
-
Mendez, R.1
Leplae, R.2
Maria, L.3
Wodak, S.J.4
-
57
-
-
0038187615
-
A protein-protein docking benchmark
-
Chen,R., Mintseris,J., Janin,J. and Weng,Z. (2003) A protein-protein docking benchmark. Proteins, 52, 88-91.
-
(2003)
Proteins
, vol.52
, pp. 88-91
-
-
Chen, R.1
Mintseris, J.2
Janin, J.3
Weng, Z.4
-
59
-
-
7544226311
-
ProDRG - A tool for high-throughput crystallography of protein-ligand complexes
-
Schuettelkopf,A.W. and van Aalten,D.M.F. (2004) ProDRG - a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr., 60, 1355-1363.
-
(2004)
Acta Crystallogr. D Biol. Crystallogr.
, vol.60
, pp. 1355-1363
-
-
Schuettelkopf, A.W.1
van Aalten, D.M.F.2
-
60
-
-
2442567233
-
Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements
-
Hayward,S. (2004) Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. J. Mol. Biol., 339, 1001-1021.
-
(2004)
J. Mol. Biol.
, vol.339
, pp. 1001-1021
-
-
Hayward, S.1
-
61
-
-
2442612037
-
Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling
-
Daidone,I., Roccatano,D. and Hayward,S. (2004) Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling. J. Mol. Biol., 339, 515-525.
-
(2004)
J. Mol. Biol.
, vol.339
, pp. 515-525
-
-
Daidone, I.1
Roccatano, D.2
Hayward, S.3
-
62
-
-
0000009443
-
Rapid comparison of protein structures
-
McLachlan,A.D. (1982) Rapid comparison of protein structures. Acta Crystallogr. A, 38, 871-873.
-
(1982)
Acta Crystallogr. A
, vol.38
, pp. 871-873
-
-
McLachlan, A.D.1
-
63
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normal mode calculations
-
Marques,O. and Sanejouand,Y.-H. (1995) Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins, 23 557-560.
-
(1995)
Proteins
, vol.23
, pp. 557-560
-
-
Marques, O.1
Sanejouand, Y.-H.2
-
64
-
-
2942511344
-
A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase
-
Cui,Q., Li,G., Ma,J. and Karplus,M. (2004) A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J. Mol. Biol., 340, 345-372.
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 345-372
-
-
Cui, Q.1
Li, G.2
Ma, J.3
Karplus, M.4
-
65
-
-
0035789518
-
Gromacs 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl,E., Hess,B. and van der Spoel,D. (2001) Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model., 7, 306-317.
-
(2001)
J. Mol. Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
66
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminski,G.A., Friesner,R.A., Tirado-Rives,J. and Jorgensen,W.L. (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B, 105, 6474-6487.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
67
-
-
1342302339
-
Conformational changes associated with protein-protein interactions
-
Goh,C.-S., Milburn,D. and Gerstein,M. (2004) Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol., 14, 104-109.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 104-109
-
-
Goh, C.-S.1
Milburn, D.2
Gerstein, M.3
-
68
-
-
0021879256
-
Crystallographic refinement of yeast tRNA-Asp
-
Westhof,E., Dumas,P. and Moras,D. (1985) Crystallographic refinement of yeast tRNA-Asp. J. Mol. Biol., 184, 119-28.
-
(1985)
J. Mol. Biol.
, vol.184
, pp. 119-128
-
-
Westhof, E.1
Dumas, P.2
Moras, D.3
|