-
1
-
-
0032718788
-
The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
-
C.W. Murray, C.A. Baxter, and A.D. Frenkel The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase J. Comput. Aided Mol. Des. 13 1999 547 562
-
(1999)
J. Comput. Aided Mol. Des.
, vol.13
, pp. 547-562
-
-
Murray, C.W.1
Baxter, C.A.2
Frenkel, A.D.3
-
2
-
-
0033559918
-
Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis
-
A.M. Davis, and S.J. Teague Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis Angew. Chem., Int. Ed. Engl. 38 1999 736 749
-
(1999)
Angew. Chem., Int. Ed. Engl.
, vol.38
, pp. 736-749
-
-
Davis, A.M.1
Teague, S.J.2
-
4
-
-
0033670301
-
Deciphering common failures in molecular docking of ligand-protein complexes
-
G.M. Verkhivker, D. Bouzida, D.K. Glhaar, P.A. Rejto, S. Arthurs, A.B. Colson, S.T. Freer, V. Larson, B.A. Luty, T. Marrone, and P.W. Rose Deciphering common failures in molecular docking of ligand-protein complexes J. Comput. Aided Mol. Des. 14 2000 731 751
-
(2000)
J. Comput. Aided Mol. Des.
, vol.14
, pp. 731-751
-
-
Verkhivker, G.M.1
Bouzida, D.2
Glhaar, D.K.3
Rejto, P.A.4
Arthurs, S.5
Colson, A.B.6
Freer, S.T.7
Larson, V.8
Luty, B.A.9
Marrone, T.10
Rose, P.W.11
-
5
-
-
0033974667
-
Accommodating protein flexibility in computational drug design
-
H.A. Carlson, and J.A. McCammon Accommodating protein flexibility in computational drug design Mol. Pharmacol. 57 2000 213 218
-
(2000)
Mol. Pharmacol.
, vol.57
, pp. 213-218
-
-
Carlson, H.A.1
McCammon, J.A.2
-
6
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
I. Halperin, B. Ma, H. Wolfson, and R. Nussinov Principles of docking: an overview of search algorithms and a guide to scoring functions Proteins 47 2002 409 443
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
8
-
-
0037666888
-
Implications of protein flexibility for drug discovery
-
S.J. Teague Implications of protein flexibility for drug discovery Nat. Rev., Drug Discov. 2 2003 527 541
-
(2003)
Nat. Rev., Drug Discov.
, vol.2
, pp. 527-541
-
-
Teague, S.J.1
-
9
-
-
0037392444
-
Issues and progress with protein kinase inhibitors for cancer treatment
-
J. Dancey, and E.A. Sausville Issues and progress with protein kinase inhibitors for cancer treatment Nat. Rev., Drug Discov. 2 2003 296 313
-
(2003)
Nat. Rev., Drug Discov.
, vol.2
, pp. 296-313
-
-
Dancey, J.1
Sausville, E.A.2
-
10
-
-
4444353636
-
Regulation of protein kinases; Controlling activity through activation segment conformation
-
B. Nolen, S. Taylor, and G. Ghosh Regulation of protein kinases; controlling activity through activation segment conformation Mol. Cell 15 2004 661 675
-
(2004)
Mol. Cell
, vol.15
, pp. 661-675
-
-
Nolen, B.1
Taylor, S.2
Ghosh, G.3
-
12
-
-
1542269006
-
PKA: A portrait of protein kinase dynamics
-
S.S. Taylor, J. Yang, J. Wu, N.M. Haste, E. Radzio-Andzelm, and G. Anand PKA: a portrait of protein kinase dynamics Biochem. Biophys. Acta 1697 2004 259 269
-
(2004)
Biochem. Biophys. Acta
, vol.1697
, pp. 259-269
-
-
Taylor, S.S.1
Yang, J.2
Wu, J.3
Haste, N.M.4
Radzio-Andzelm, E.5
Anand, G.6
-
13
-
-
14544284010
-
The protein kinase resource: Everything you always wanted to know about protein kinases but were afraid to ask
-
C. Petretti, and C. Prigent The protein kinase resource: everything you always wanted to know about protein kinases but were afraid to ask Biol. Cell 97 2005 113 118
-
(2005)
Biol. Cell
, vol.97
, pp. 113-118
-
-
Petretti, C.1
Prigent, C.2
-
14
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
I.D. Kuntz, J. Blaney, S. Oatley, R. Langridge, and T. Ferrin A geometric approach to macromolecule-ligand interactions J. Mol. Biol. 161 1982 269 280
-
(1982)
J. Mol. Biol.
, vol.161
, pp. 269-280
-
-
Kuntz, I.D.1
Blaney, J.2
Oatley, S.3
Langridge, R.4
Ferrin, T.5
-
15
-
-
0029937340
-
Molecular docking using surface complementarity
-
V. Sobolev, R. Wade, G. Vriend, and M. Edelman Molecular docking using surface complementarity Proteins 25 1996 120 129
-
(1996)
Proteins
, vol.25
, pp. 120-129
-
-
Sobolev, V.1
Wade, R.2
Vriend, G.3
Edelman, M.4
-
16
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
M. Rarey, B. Kramer, T. Lengauer, and G. Klebe A fast flexible docking method using an incremental construction algorithm J. Mol. Biol. 261 1996 470 479
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 470-479
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
18
-
-
0035416126
-
High-throughput docking for lead generation
-
R. Abgayan, and M. Totrov High-throughput docking for lead generation Curr. Opin. Chem. Biol. 5 2001 372 382
-
(2001)
Curr. Opin. Chem. Biol.
, vol.5
, pp. 372-382
-
-
Abgayan, R.1
Totrov, M.2
-
19
-
-
1442351132
-
Protein flexibility in ligand docking and virtual screening to protein kinases
-
C.N. Cavasotto, and R.A. Abagyan Protein flexibility in ligand docking and virtual screening to protein kinases J. Mol. Biol. 337 2004 209 225
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 209-225
-
-
Cavasotto, C.N.1
Abagyan, R.A.2
-
23
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sanchez, F. Melo, and A. Sali Comparative protein structure modeling of genes and genomes Annu. Rev. Biophys. Biomol. Struct. 29 2000 291 325
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
24
-
-
0028158936
-
Ligand docking to proteins with discrete side-chain flexibility
-
A. Leach Ligand docking to proteins with discrete side-chain flexibility J. Mol. Biol. 235 1995 345 356
-
(1995)
J. Mol. Biol.
, vol.235
, pp. 345-356
-
-
Leach, A.1
-
25
-
-
0035957528
-
FlexE: Efficient molecular docking considering protein structure variations
-
H. Clausen, C. Buning, M. Rarey, and T. Lengauer FlexE: efficient molecular docking considering protein structure variations J. Mol. Biol. 308 2001 377 395
-
(2001)
J. Mol. Biol.
, vol.308
, pp. 377-395
-
-
Clausen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
26
-
-
0031581852
-
Molecular docking to ensembles of protein structures
-
R.M.A. Knegtel, I.D. Kuntz, and C.M. Oshiro Molecular docking to ensembles of protein structures J. Mol. Biol. 266 1997 424 440
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 424-440
-
-
Knegtel, R.M.A.1
Kuntz, I.D.2
Oshiro, C.M.3
-
27
-
-
0036137713
-
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
-
F. Osterberg, G.M. Morris, M.F. Sanner, A.J. Olson, and D.S. Goodsell Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock Proteins 46 2002 34 40
-
(2002)
Proteins
, vol.46
, pp. 34-40
-
-
Osterberg, F.1
Morris, G.M.2
Sanner, M.F.3
Olson, A.J.4
Goodsell, D.S.5
-
28
-
-
0000302276
-
Application of a molecular dynamics simulation method with a generalized effective potential to the flexible molecular docking problems
-
Y. Pak, and S. Wang Application of a molecular dynamics simulation method with a generalized effective potential to the flexible molecular docking problems J. Phys. Chem., B 104 2000 354 359
-
(2000)
J. Phys. Chem., B
, vol.104
, pp. 354-359
-
-
Pak, Y.1
Wang, S.2
-
29
-
-
0033135477
-
Docking of flexible ligands to flexible receptors in solution using molecular dynamics simulations
-
M. Mangoni, D. Roccatano, and A. Di Nola Docking of flexible ligands to flexible receptors in solution using molecular dynamics simulations Proteins 35 1999 153 162
-
(1999)
Proteins
, vol.35
, pp. 153-162
-
-
Mangoni, M.1
Roccatano, D.2
Di Nola, A.3
-
30
-
-
29144441461
-
Refinement of protein cores and protein-peptide interfaces using a potential scaling approach
-
(in press).
-
R.N. Riemann, M. Zacharias, Refinement of protein cores and protein-peptide interfaces using a potential scaling approach, Prot. Eng. (in press).
-
Prot. Eng.
-
-
Riemann, R.N.1
Zacharias, M.2
-
31
-
-
0001105311
-
Method for including the dynamic fluctuations of a protein in computer-aided drug design
-
H.A. Carlson, K.M. Masukawa, and J.A. McCammon Method for including the dynamic fluctuations of a protein in computer-aided drug design J. Phys. Chem., A 103 1999 10213 10219
-
(1999)
J. Phys. Chem., a
, vol.103
, pp. 10213-10219
-
-
Carlson, H.A.1
Masukawa, K.M.2
McCammon, J.A.3
-
32
-
-
0037157153
-
Computational drug design accommodating receptor flexibility: The relaxed complex scheme
-
J.H. Lin, A.L. Perryman, J.R. Schames, and J.A. McCammon Computational drug design accommodating receptor flexibility: the relaxed complex scheme J. Am. Chem. Soc. 124 2002 5632 5633
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 5632-5633
-
-
Lin, J.H.1
Perryman, A.L.2
Schames, J.R.3
McCammon, J.A.4
-
33
-
-
0032466036
-
A method for biomolecular structural recognition and docking allowing conformational flexibility
-
B. Sandak, R. Nussinov, and H.J. Wolfson A method for biomolecular structural recognition and docking allowing conformational flexibility J. Comput. Biol. 5 1998 631 654
-
(1998)
J. Comput. Biol.
, vol.5
, pp. 631-654
-
-
Sandak, B.1
Nussinov, R.2
Wolfson, H.J.3
-
34
-
-
0032147007
-
Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers
-
B. Sandak, H.J. Wolfson, and R. Nussinov Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers Proteins: Struct. Funct., Genet. 32 1998 159 174
-
(1998)
Proteins: Struct. Funct., Genet.
, vol.32
, pp. 159-174
-
-
Sandak, B.1
Wolfson, H.J.2
Nussinov, R.3
-
35
-
-
0001147249
-
Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Applications to DNA minor groove ligand complex
-
M. Zacharias, and H. Sklenar Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: applications to DNA minor groove ligand complex J. Comput. Chem. 20 1999 287 300
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 287-300
-
-
Zacharias, M.1
Sklenar, H.2
-
36
-
-
0035915338
-
Fully flexible low-mode docking: Application to induced fit in HIV integrase
-
G.M. Keseru, and I. Kolossvary Fully flexible low-mode docking: application to induced fit in HIV integrase J. Am. Chem. Soc. 123 2001 12708 12709
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 12708-12709
-
-
Keseru, G.M.1
Kolossvary, I.2
-
37
-
-
9244235496
-
A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor
-
R. Tatsumi, Y. Fukunishi, and H. Nakamura A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor J. Comput. Chem. 25 2004 1995 2005
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1995-2005
-
-
Tatsumi, R.1
Fukunishi, Y.2
Nakamura, H.3
-
39
-
-
1542316339
-
Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP
-
M. Zacharias Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP Proteins: Struct., Funct., Genet. 54 2004 759 767
-
(2004)
Proteins: Struct., Funct., Genet.
, vol.54
, pp. 759-767
-
-
Zacharias, M.1
-
40
-
-
0025826967
-
Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex
-
G.D. Van Duyne, R.F. Standaert, P.A. Karplus, S.L. Schreiber, and J. Clardy Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex Science 252 1991 839 842
-
(1991)
Science
, vol.252
, pp. 839-842
-
-
Van Duyne, G.D.1
Standaert, R.F.2
Karplus, P.A.3
Schreiber, S.L.4
Clardy, J.5
-
41
-
-
0025826966
-
Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin
-
S.W. Michnick, M.K. Rosen, T.J. Wandless, M. Karplus, and S.L. Schreiber Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin Science 252 1991 836 839
-
(1991)
Science
, vol.252
, pp. 836-839
-
-
Michnick, S.W.1
Rosen, M.K.2
Wandless, T.J.3
Karplus, M.4
Schreiber, S.L.5
-
42
-
-
0000838678
-
Comparative X-ray structures of the major protein for the immunosuppressant FK506 (Tacrolimus) in unliganded form and in complex with FK506 and rapamycin
-
K.P. Wilson, M.M. Yamashita, M.D. Sintchak, S.H. Rotstein, M.A. Murcko, J. Boger, J.A. Thomson, M.J. Fitzgibbon, and M.A. Navia Comparative X-ray structures of the major protein for the immunosuppressant FK506 (Tacrolimus) in unliganded form and in complex with FK506 and rapamycin Acta Crystallogr., Sect. D 51 1995 511 522
-
(1995)
Acta Crystallogr., Sect. D
, vol.51
, pp. 511-522
-
-
Wilson, K.P.1
Yamashita, M.M.2
Sintchak, M.D.3
Rotstein, S.H.4
Murcko, M.A.5
Boger, J.6
Thomson, J.A.7
Fitzgibbon, M.J.8
Navia, M.A.9
-
43
-
-
15244355250
-
The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
-
G.R. Smith, M.J. Sternberg, and P.A. Bates The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking J. Mol. Biol. 347 2005 1077 1101
-
(2005)
J. Mol. Biol.
, vol.347
, pp. 1077-1101
-
-
Smith, G.R.1
Sternberg, M.J.2
Bates, P.A.3
-
44
-
-
0001295503
-
Principal component analysis and long time protein dynamics
-
M.A. Balsera, W. Wriggers, Y. Oono, and K. Schulten Principal component analysis and long time protein dynamics J. Phys. Chem. 100 1996 2567 2572
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 2567-2572
-
-
Balsera, M.A.1
Wriggers, W.2
Oono, Y.3
Schulten, K.4
-
45
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
I. Bahar, A.R. Atilgan, and B. Erman Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential Folding Des. 2 1997 173 181
-
(1997)
Folding Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
46
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
K. Hinsen Analysis of domain motions by approximate normal mode calculations Proteins 33 1998 417 429
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
47
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
F. Tama, and Y.H. Sanejouand Conformational change of proteins arising from normal mode calculations Protein Eng. 14 2001 1 6
-
(2001)
Protein Eng.
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
48
-
-
0030596012
-
Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease a
-
B. Kobe, and J. Deisenhofer Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A J. Mol. Biol. 264 1996 1028 1043
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 1028-1043
-
-
Kobe, B.1
Deisenhofer, J.2
-
49
-
-
0027718173
-
Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats
-
B. Kobe, and J. Deisenhofer Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats Nature 366 1993 751 756
-
(1993)
Nature
, vol.366
, pp. 751-756
-
-
Kobe, B.1
Deisenhofer, J.2
-
50
-
-
0038583687
-
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
-
M. Zacharias Protein-protein docking with a reduced protein model accounting for side-chain flexibility Proteins Sci. 12 2003 1271 1282
-
(2003)
Proteins Sci.
, vol.12
, pp. 1271-1282
-
-
Zacharias, M.1
-
51
-
-
0037436388
-
Dynamic features of cAMP-dependent protein kinase revealed by apoenzyme crystal structure
-
P. Akamine, P. Madhusudan, J. Wu, N.H. Xuong, L.F. Ten Eyck, and S.S. Taylor Dynamic features of cAMP-dependent protein kinase revealed by apoenzyme crystal structure J. Mol. Biol. 327 2003 159 171
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 159-171
-
-
Akamine, P.1
Madhusudan, P.2
Wu, J.3
Xuong, N.H.4
Ten Eyck, L.F.5
Taylor, S.S.6
-
52
-
-
0031574365
-
Staurosporine-induced conformational changes of cAMP-dependent protein kinase catalytic subunit explain inhibitory potential
-
L. Prade, R.A. Engh, A. Girod, V. Kinzel, R. Huber, and D. Bossemeyer Staurosporine-induced conformational changes of cAMP-dependent protein kinase catalytic subunit explain inhibitory potential Structure 5 1997 1627 1637
-
(1997)
Structure
, vol.5
, pp. 1627-1637
-
-
Prade, L.1
Engh, R.A.2
Girod, A.3
Kinzel, V.4
Huber, R.5
Bossemeyer, D.6
|