-
1
-
-
0033974667
-
Accommodating protein flexibility in computational drug design
-
Carlson H.A., McCammon J.A. 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
-
2
-
-
0001105311
-
Method for including the dynamic fluctuations of a protein in computer-aided drug design
-
Carlson H.A., Masukawa K.M., McCammon J.A. Method for including the dynamic fluctuations of a protein in computer-aided drug design. J Phys Chem A. 103:1999;10 213-10 219.
-
(1999)
J Phys Chem a
, vol.103
, pp. 10213-10219
-
-
Carlson, H.A.1
Masukawa, K.M.2
McCammon, J.A.3
-
3
-
-
0033135477
-
Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation
-
Mangoni M., Roccatano D., Nola A.D. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation. Proteins. 35:1999;153-162.
-
(1999)
Proteins
, vol.35
, pp. 153-162
-
-
Mangoni, M.1
Roccatano, D.2
Nola, A.D.3
-
4
-
-
0032738842
-
Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
-
Kramer B., Rarey M., Lengauer T. Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins. 37:1999;228-241.
-
(1999)
Proteins
, vol.37
, pp. 228-241
-
-
Kramer, B.1
Rarey, M.2
Lengauer, T.3
-
5
-
-
0032718788
-
The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
-
Murray C.W., Baxter C.A., Frenkel A.D. 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
-
6
-
-
0032708785
-
Efficacy and selectivity in flexible database docking
-
Knegtel R.M.A., Wagener M. Efficacy and selectivity in flexible database docking. Proteins. 37:1999;334-345.
-
(1999)
Proteins
, vol.37
, pp. 334-345
-
-
Knegtel, R.M.A.1
Wagener, M.2
-
7
-
-
0032899364
-
The effect of multiple binding modes on empirical modeling of ligand docking to proteins
-
Brem R., Dill K.A. The effect of multiple binding modes on empirical modeling of ligand docking to proteins. Protein Sci. 8:1999;1134-1143.
-
(1999)
Protein Sci
, vol.8
, pp. 1134-1143
-
-
Brem, R.1
Dill, K.A.2
-
8
-
-
0032961895
-
The particle concept: Placing discrete water molecules during protein-ligand docking predictions
-
Rarey M., Kramer B., Lengauer T. The particle concept: placing discrete water molecules during protein-ligand docking predictions. Proteins. 34:1999;17-28.
-
(1999)
Proteins
, vol.34
, pp. 17-28
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
-
9
-
-
0033214412
-
Exhaustive docking of molecular fragments with electrostatic solvation
-
Majeux N., Scarsi M., Apostolakis J., Ehrhardt C., Caflisch A. Exhaustive docking of molecular fragments with electrostatic solvation. Proteins. 37:1999;88-105.
-
(1999)
Proteins
, vol.37
, pp. 88-105
-
-
Majeux, N.1
Scarsi, M.2
Apostolakis, J.3
Ehrhardt, C.4
Caflisch, A.5
-
10
-
-
0032993815
-
Scoring functions: A view from the bench
-
Tame J.R.H. Scoring functions: a view from the bench. J Comput Aided Mol Des. 13:1999;99-108.
-
(1999)
J Comput Aided Mol des
, vol.13
, pp. 99-108
-
-
Tame, J.R.H.1
-
11
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
Gohlke H., Hendlich M., Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol. 295:2000;337-356.
-
(2000)
J Mol Biol
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
12
-
-
0033545622
-
A general and fast scoring function for protein-ligand interactions: A simplified potential approach
-
Muegge I., Martin Y.C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem. 42:1999;791-804.
-
(1999)
J Med Chem
, vol.42
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
13
-
-
0000823044
-
BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential
-
Mitchell J.B.O., Laskowski R.A., Alex A., Thornton J.M. BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential. J Comput Chem. 20:1999;1165-1176.
-
(1999)
J Comput Chem
, vol.20
, pp. 1165-1176
-
-
Mitchell, J.B.O.1
Laskowski, R.A.2
Alex, A.3
Thornton, J.M.4
-
14
-
-
0000823044
-
BLEEP - potential of mean force describing protein-ligand interactions: 11. Calculation of binding energies and comparison with experimental data
-
Mitchell J.B.O., Laskowski R.A., Alex A., Forster M.J., Thornton J.M. BLEEP - potential of mean force describing protein-ligand interactions: 11. Calculation of binding energies and comparison with experimental data. J Comput Chem. 20:1999;1165-1176.
-
(1999)
J Comput Chem
, vol.20
, pp. 1165-1176
-
-
Mitchell, J.B.O.1
Laskowski, R.A.2
Alex, A.3
Forster, M.J.4
Thornton, J.M.5
-
15
-
-
0032855301
-
MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
-
Liu M., Wang S. MCDOCK: a Monte Carlo simulation approach to the molecular docking problem. J Comput Aided Mol Des. 13:1999;435-451.
-
(1999)
J Comput Aided Mol des
, vol.13
, pp. 435-451
-
-
Liu, M.1
Wang, S.2
-
16
-
-
0345483185
-
Prodock: Software package for protein modeling and docking
-
Trosset J.Y., Scheraga H.A. Prodock: software package for protein modeling and docking. J Comput Chem. 20:1999;412-427.
-
(1999)
J Comput Chem
, vol.20
, pp. 412-427
-
-
Trosset, J.Y.1
Scheraga, H.A.2
-
17
-
-
0032840569
-
DREAM++: Flexible docking program for virtual combinatorial libraries
-
Makino S., Ewing T.J.A., Kuntz I.D. DREAM++: flexible docking program for virtual combinatorial libraries. J Comput Aided Mol Des. 13:1999;513-532.
-
(1999)
J Comput Aided Mol des
, vol.13
, pp. 513-532
-
-
Makino, S.1
Ewing, T.J.A.2
Kuntz, I.D.3
-
18
-
-
0033044392
-
Integration of combinatorial chemistry and structure based drug design
-
Antel J. Integration of combinatorial chemistry and structure based drug design. Curr Opin Drug Discov Dev. 2:1999;224-233.
-
(1999)
Curr Opin Drug Discov Dev
, vol.2
, pp. 224-233
-
-
Antel, J.1
-
19
-
-
0033559918
-
Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis
-
Davis A.M., Teague S.J. 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
-
20
-
-
0033574397
-
The discovery of steroids and other novel FKBP inhibitors using a molecular docking program
-
Burkhard P., Hommel U., Sanner M., Walkinshaw M.D. The discovery of steroids and other novel FKBP inhibitors using a molecular docking program. J Mol Biol. 287:1999;853-858.
-
(1999)
J Mol Biol
, vol.287
, pp. 853-858
-
-
Burkhard, P.1
Hommel, U.2
Sanner, M.3
Walkinshaw, M.D.4
-
21
-
-
84991422777
-
-
DockCrunch on World Wide Web URL
-
DockCrunch on World Wide Web URL: http://www.protherics.com/crunch.
-
-
-
-
22
-
-
0033967525
-
Theoretical investigation of substrate specificity for cytochromes P450 IA2, P450 IID6 and P450 IIIA4
-
De Rienzo F., Fanelli F., Menziani M.C., De Benedetti P.G. Theoretical investigation of substrate specificity for cytochromes P450 IA2, P450 IID6 and P450 IIIA4. J Comput Aided Mol Des. 14:2000;93-116.
-
(2000)
J Comput Aided Mol des
, vol.14
, pp. 93-116
-
-
De Rienzo, F.1
Fanelli, F.2
Menziani, M.C.3
De Benedetti, P.G.4
-
23
-
-
13044300859
-
Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes
-
Matthews D.A., Dragovich P.S., Webber S.E., Fuhrman S.A., Patick A.K., Zalman L.S., Hendrickson T.F., Love R.A., Prins T.J., Marakovits J.T.et al. Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. Proc Natl Acad Sci USA. 96:1999;11 000-11 007.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 11000-11007
-
-
Matthews, D.A.1
Dragovich, P.S.2
Webber, S.E.3
Fuhrman, S.A.4
Patick, A.K.5
Zalman, L.S.6
Hendrickson, T.F.7
Love, R.A.8
Prins, T.J.9
Marakovits, J.T.10
-
24
-
-
0033523954
-
Design, synthesis, and biological evaluation of potent thiazine- And thiazepine-based matrix metalloproteinase inhibitors
-
Almstead N.G., Bradley R.S., Pikul S., De B., Natchus M.G., Taiwo Y.O., Gu F., Williams L.E., Hynd B.A., Janusz M.J.et al. Design, synthesis, and biological evaluation of potent thiazine- and thiazepine-based matrix metalloproteinase inhibitors. J Med Chem. 42:1999;4547-4562.
-
(1999)
J Med Chem
, vol.42
, pp. 4547-4562
-
-
Almstead, N.G.1
Bradley, R.S.2
Pikul, S.3
De, B.4
Natchus, M.G.5
Taiwo, Y.O.6
Gu, F.7
Williams, L.E.8
Hynd, B.A.9
Janusz, M.J.10
-
25
-
-
0033619976
-
Design, synthesis, and biological evaluation of matrix metalloproteinase inhibitors derived from a modified proline scaffold
-
Cheng M., De B., Almstead N.G., Pikul S.G., Dowty M.E., Dietsch C.R., Dunaway C.M., Gu F., Hsieh L.C., Janusz M.J.et al. Design, synthesis, and biological evaluation of matrix metalloproteinase inhibitors derived from a modified proline scaffold. J Med Chem. 42:1999;5426-5436.
-
(1999)
J Med Chem
, vol.42
, pp. 5426-5436
-
-
Cheng, M.1
De, B.2
Almstead, N.G.3
Pikul, S.G.4
Dowty, M.E.5
Dietsch, C.R.6
Dunaway, C.M.7
Gu, F.8
Hsieh, L.C.9
Janusz, M.J.10
-
26
-
-
0034628453
-
Design and synthesis of piperazine-based matrix metallo-proteinase inhibitors
-
Cheng M., De B., Pikul S., Almstead N.G., Natchus M.G., Anastasio M.V., McPhail S.J., Snider C.E., Taiwo Y.O., Chen L.et al. Design and synthesis of piperazine-based matrix metallo-proteinase inhibitors. J Med Chem. 43:2000;369-380.
-
(2000)
J Med Chem
, vol.43
, pp. 369-380
-
-
Cheng, M.1
De, B.2
Pikul, S.3
Almstead, N.G.4
Natchus, M.G.5
Anastasio, M.V.6
McPhail, S.J.7
Snider, C.E.8
Taiwo, Y.O.9
Chen, L.10
-
27
-
-
0344731437
-
Structure-based design, synthesis, and X-ray crystallography of a high-affinity antagonist of the Grb2-SH2 domain containing an asparagine mimetic
-
Furet P., García-Echeverría C., Gay B., Schoepfer J., Zeller M., Rahuel J. Structure-based design, synthesis, and X-ray crystallography of a high-affinity antagonist of the Grb2-SH2 domain containing an asparagine mimetic. J Med Chem. 42:1999;2358-2363.
-
(1999)
J Med Chem
, vol.42
, pp. 2358-2363
-
-
Furet, P.1
García-Echeverría, C.2
Gay, B.3
Schoepfer, J.4
Zeller, M.5
Rahuel, J.6
-
29
-
-
0033551233
-
Structure-based design of sub-micromolar, biologically active inhibitors of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase
-
Aronov A.M., Suresh S., Buckner F.S., Van Voorhis W.C., Verlinde C.L.M.J., Opperdoes F.R., Hol W.G.J., Gelb M.H. Structure-based design of sub-micromolar, biologically active inhibitors of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase. Proc Natl Acad Sci USA. 96:1999;4273-4278.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 4273-4278
-
-
Aronov, A.M.1
Suresh, S.2
Buckner, F.S.3
Van Voorhis, W.C.4
Verlinde, C.L.M.J.5
Opperdoes, F.R.6
Hol, W.G.J.7
Gelb, M.H.8
-
30
-
-
0033047131
-
Structure-based discovery of tipranavir disodium (PNU-140690E): A potent, oral bio-available, non-peptidic HIV protease inhibitor
-
Thaisrivongs S., Strohbach J.W. Structure-based discovery of tipranavir disodium (PNU-140690E): a potent, oral bio-available, non-peptidic HIV protease inhibitor. Biopolymers. 51:1999;51-58.
-
(1999)
Biopolymers
, vol.51
, pp. 51-58
-
-
Thaisrivongs, S.1
Strohbach, J.W.2
-
33
-
-
0034629461
-
Re-engineering of human urokinase provides a system for structure-based drug design at high resolution and reveals a novel structural subsite
-
Nienaber V., Wang J., Davidson D., Henkin J. Re-engineering of human urokinase provides a system for structure-based drug design at high resolution and reveals a novel structural subsite. J Biol Chem. 275:2000;7239-7248.
-
(2000)
J Biol Chem
, vol.275
, pp. 7239-7248
-
-
Nienaber, V.1
Wang, J.2
Davidson, D.3
Henkin, J.4
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