-
1
-
-
0002716826
-
Structure-based design of enzyme inhibitors and receptor ligands
-
Kubinyi H. Structure-based design of enzyme inhibitors and receptor ligands. Curr. Opin. Drug Discov. Devel. 1:1998;4-15.
-
(1998)
Curr. Opin. Drug Discov. Devel.
, vol.1
, pp. 4-15
-
-
Kubinyi, H.1
-
2
-
-
0034813214
-
Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase
-
Fritz T.A., Tondi D., Finer-Moore J.S., Costi M.P., Stroud R.M. Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase. Chem. Biol. 131:2001;1-15.
-
(2001)
Chem. Biol.
, vol.131
, pp. 1-15
-
-
Fritz, T.A.1
Tondi, D.2
Finer-Moore, J.S.3
Costi, M.P.4
Stroud, R.M.5
-
3
-
-
0346278965
-
Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking
-
Anderson A.C., O'Neil R.H., Surti T.S., Stroud R.M. Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking. Chem. Biol. 88:2001;1-13.
-
(2001)
Chem. Biol.
, vol.88
, pp. 1-13
-
-
Anderson, A.C.1
O'Neil, R.H.2
Surti, T.S.3
Stroud, R.M.4
-
4
-
-
0029643784
-
The complex of anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 Å resolution: Implications for a new mode of inhibition
-
Stout T.J., Stroud R.M. The complex of anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 Å resolution. implications for a new mode of inhibition Structure. 1:1996;67-77.
-
(1996)
Structure
, vol.1
, pp. 67-77
-
-
Stout, T.J.1
Stroud, R.M.2
-
5
-
-
0033559918
-
Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis
-
Davis M., Teague T.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, M.1
Teague, T.J.2
-
6
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
-
Ma B., Shatsky M., Wolfson H.J., Nussinov R. Multiple diverse ligands binding at a single protein site. a matter of pre-existing populations Protein Sci. 11:2002;184-197.
-
(2002)
Protein Sci.
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.J.3
Nussinov, R.4
-
7
-
-
0037470496
-
Antibody multispecificity mediated by conformational diversity
-
James L.C., Roversi P., Tawfik D.S. Antibody multispecificity mediated by conformational diversity. Science. 299:2003;1362-1367.
-
(2003)
Science
, vol.299
, pp. 1362-1367
-
-
James, L.C.1
Roversi, P.2
Tawfik, D.S.3
-
8
-
-
0033289634
-
Database screening for HIV protease ligands: The influence of binding-site conformation and representation on ligand selectivity
-
T. Lengauer, R. Schneider, P. Bork, D. Brutlag, J. Glasgow, H.W. Mewes, and R. Zimmer (eds), Menlo Park, CA
-
Schnecke, V., and Kuhn, L.A. (1999). Database screening for HIV protease ligands: the influence of binding-site conformation and representation on ligand selectivity, p. 242-251. In T. Lengauer, R. Schneider, P. Bork, D. Brutlag, J. Glasgow, H.W. Mewes, and R. Zimmer (eds) Proceeding of the Seventh International Conference on Intelligent Systems for Molecular Biology, Menlo Park, CA.
-
(1999)
Proceeding of the Seventh International Conference on Intelligent Systems for Molecular Biology
, pp. 242-251
-
-
Schnecke, V.1
Kuhn, L.A.2
-
9
-
-
0031965676
-
Flexible ligand docking using conformational ensembles
-
Lorber D.M., Shoichet B.K. Flexible ligand docking using conformational ensembles. Protein Sci. 7:1998;938-950.
-
(1998)
Protein Sci.
, vol.7
, pp. 938-950
-
-
Lorber, D.M.1
Shoichet, B.K.2
-
10
-
-
0036019065
-
Protein flexibility is an important component of structure-based drug discovery
-
Carlson H.A. Protein flexibility is an important component of structure-based drug discovery. Curr. Pharm. Des. 8:2002;1571-1578.
-
(2002)
Curr. Pharm. Des.
, vol.8
, pp. 1571-1578
-
-
Carlson, H.A.1
-
13
-
-
0542362994
-
Rate theory for gated diffusion-influenced ligand binding to proteins
-
Northrup S.H., McCammon J.A. Rate theory for gated diffusion-influenced ligand binding to proteins. J. Phys. Chem. 86:1982;2314-2321.
-
(1982)
J. Phys. Chem.
, vol.86
, pp. 2314-2321
-
-
Northrup, S.H.1
McCammon, J.A.2
-
14
-
-
0037130289
-
Structure-based studies on species-specific inhibition of thymidylate synthase
-
Costi M.P., Tondi D., Rinaldi M., Barlocco D., Pecorari P., Soragni F., Venturelli A., Stroud R.M. Structure-based studies on species-specific inhibition of thymidylate synthase. Biochim. Biophys. Acta. 1587:2002;206-214.
-
(2002)
Biochim. Biophys. Acta
, vol.1587
, pp. 206-214
-
-
Costi, M.P.1
Tondi, D.2
Rinaldi, M.3
Barlocco, D.4
Pecorari, P.5
Soragni, F.6
Venturelli, A.7
Stroud, R.M.8
-
15
-
-
0030964552
-
Specificity in structure-based drug design: Identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase
-
Gschwend D.A., Sirawaraporn W., Santi D.V., Kuntz I.D. Specificity in structure-based drug design. identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase Proteins. 29:1997;59-67.
-
(1997)
Proteins
, vol.29
, pp. 59-67
-
-
Gschwend, D.A.1
Sirawaraporn, W.2
Santi, D.V.3
Kuntz, I.D.4
-
16
-
-
0034966704
-
Enzyme specificity under dynamic control II: Principal component analysis of α-litic protease using global and local solvent boundary conditions
-
Ota N., Agard D.A. Enzyme specificity under dynamic control II. principal component analysis of α-litic protease using global and local solvent boundary conditions Protein Sci. 10:2001;1403-1414.
-
(2001)
Protein Sci.
, vol.10
, pp. 1403-1414
-
-
Ota, N.1
Agard, D.A.2
-
17
-
-
0037457982
-
Conformational dynamics along the enzymatic reaction pathway: Thymidylate synthase, "the movie."
-
Stroud R.M., Finer-Moore J.S. Conformational dynamics along the enzymatic reaction pathway. thymidylate synthase, "the movie." Biochemistry. 42:2003;239-247.
-
(2003)
Biochemistry
, vol.42
, pp. 239-247
-
-
Stroud, R.M.1
Finer-Moore, J.S.2
-
18
-
-
0029036377
-
The catalytic mechanism and structure of thymidylate synthase
-
Carreras C.W., Santi D.V. The catalytic mechanism and structure of thymidylate synthase. Annu. Rev. Biochem. 64:1995;721-762.
-
(1995)
Annu. Rev. Biochem.
, vol.64
, pp. 721-762
-
-
Carreras, C.W.1
Santi, D.V.2
-
19
-
-
0033514283
-
Structure-based design of inhibitors specific for bacterial thymidylate synthase
-
Stout T.J., Tondi D., Rinaldi M., Barlocco D., Pecorari P., Santi D.V., Kuntz I.D., Stroud R.M., Shoichet B.K., Costi M.P. Structure-based design of inhibitors specific for bacterial thymidylate synthase. Biochemistry. 38:1999;1607-1617.
-
(1999)
Biochemistry
, vol.38
, pp. 1607-1617
-
-
Stout, T.J.1
Tondi, D.2
Rinaldi, M.3
Barlocco, D.4
Pecorari, P.5
Santi, D.V.6
Kuntz, I.D.7
Stroud, R.M.8
Shoichet, B.K.9
Costi, M.P.10
-
20
-
-
0023121146
-
Atomic structure of thymidylate synthase: Target for rational drug design
-
Hardy L.W., Finer-Moore J.S., Montfort W.R., Jones M.O., Santi D.V., Stroud R.M. Atomic structure of thymidylate synthase. target for rational drug design Science. 235:1987;448-455.
-
(1987)
Science
, vol.235
, pp. 448-455
-
-
Hardy, L.W.1
Finer-Moore, J.S.2
Montfort, W.R.3
Jones, M.O.4
Santi, D.V.5
Stroud, R.M.6
-
22
-
-
0027171350
-
Refined structure of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei
-
Finer-Moore J.S., Fauman E.B., Foster P.G., Perry K.M., Santi D.V., Stroud R.M. Refined structure of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei. J. Mol. Biol. 232:1993;1101-1116.
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 1101-1116
-
-
Finer-Moore, J.S.1
Fauman, E.B.2
Foster, P.G.3
Perry, K.M.4
Santi, D.V.5
Stroud, R.M.6
-
24
-
-
0030931612
-
Prediction of protein conformational freedom from distance constraints
-
De Groot B.L., Van Aalten D.M.F., Scheek R.M., Amadei A., Vriend G., Berendsen H.J.C. Prediction of protein conformational freedom from distance constraints. Proteins. 29:1997;240-251.
-
(1997)
Proteins
, vol.29
, pp. 240-251
-
-
De Groot, B.L.1
Van Aalten, D.M.F.2
Scheek, R.M.3
Amadei, A.4
Vriend, G.5
Berendsen, H.J.C.6
-
25
-
-
0033577983
-
Phthalein derivatives as a new tool for selectivity in thymidylate synthase inhibition
-
Costi M.P., Rinaldi M., Tondi D., Pecorari P., Barlocco D., Ghelli S., Stroud R.M., Santi D.V., Stout T.J., Musiu C.et al. Phthalein derivatives as a new tool for selectivity in thymidylate synthase inhibition. J. Med. Chem. 42:1999;2112-2124.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 2112-2124
-
-
Costi, M.P.1
Rinaldi, M.2
Tondi, D.3
Pecorari, P.4
Barlocco, D.5
Ghelli, S.6
Stroud, R.M.7
Santi, D.V.8
Stout, T.J.9
Musiu, C.10
-
26
-
-
0025615583
-
Plastic adaptation toward mutations in proteins: Structural comparison of thymidylate synthases
-
Perry K.M., Fauman E.B., Finer-Moore J.S., Montfort W.R., Maley G.F., Maley F., Stroud R.M. Plastic adaptation toward mutations in proteins. structural comparison of thymidylate synthases Proteins. 8:1990;315-333.
-
(1990)
Proteins
, vol.8
, pp. 315-333
-
-
Perry, K.M.1
Fauman, E.B.2
Finer-Moore, J.S.3
Montfort, W.R.4
Maley, G.F.5
Maley, F.6
Stroud, R.M.7
-
27
-
-
0027522358
-
Structure-based discovery of inhibitors of thymidylate synthase
-
Shoichet B.K., Stroud R.M., Santi D.V., Kuntz I.D., Perry K.M. Structure-based discovery of inhibitors of thymidylate synthase. Science. 259:1993;1445-1450.
-
(1993)
Science
, vol.259
, pp. 1445-1450
-
-
Shoichet, B.K.1
Stroud, R.M.2
Santi, D.V.3
Kuntz, I.D.4
Perry, K.M.5
-
28
-
-
0025311258
-
Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate
-
Montfort W.R., Perry K.M., Fauman E.B., Finer-Moore J.S., Maley G.F., Hardy L., Maley F., Stroud R.M. Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate. Biochemistry. 29:1990;6964-6977.
-
(1990)
Biochemistry
, vol.29
, pp. 6964-6977
-
-
Montfort, W.R.1
Perry, K.M.2
Fauman, E.B.3
Finer-Moore, J.S.4
Maley, G.F.5
Hardy, L.6
Maley, F.7
Stroud, R.M.8
-
29
-
-
0035916215
-
Human thymidylate synthase is in the closed conformation when complexed with dUMP and Raltitrexed, an antifolate drug
-
Phan J., Koli S., Minor W., Dunlap R.B., Berger S.H., Lebioda L. Human thymidylate synthase is in the closed conformation when complexed with dUMP and Raltitrexed, an antifolate drug. Biochemistry. 40:2001;1897-1902.
-
(2001)
Biochemistry
, vol.40
, pp. 1897-1902
-
-
Phan, J.1
Koli, S.2
Minor, W.3
Dunlap, R.B.4
Berger, S.H.5
Lebioda, L.6
-
30
-
-
0035061447
-
Crystal structure of a deletion mutant of human thymidylate synthase Δ(7-29) and its ternary complex with Tomudex and dUMP
-
Almog R., Waddling C.A., Maley F., Maley G.F., Van Roey P. Crystal structure of a deletion mutant of human thymidylate synthase Δ(7-29) and its ternary complex with Tomudex and dUMP. Protein Sci. 10:2001;988-996.
-
(2001)
Protein Sci.
, vol.10
, pp. 988-996
-
-
Almog, R.1
Waddling, C.A.2
Maley, F.3
Maley, G.F.4
Van Roey, P.5
-
31
-
-
0028403267
-
Structure of and kinetic channelling in bifunctional dihydrofolate reductase-thymidylate synthase
-
Knighton D.R., Kan C.C., Howland E., Janson C.A., Hostomska Z., Welsh K.M., Matthews D.A. Structure of and kinetic channelling in bifunctional dihydrofolate reductase-thymidylate synthase. Nat. Struct. Biol. 1:1994;186-194.
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 186-194
-
-
Knighton, D.R.1
Kan, C.C.2
Howland, E.3
Janson, C.A.4
Hostomska, Z.5
Welsh, K.M.6
Matthews, D.A.7
-
32
-
-
0345426287
-
The structural mechanism for half-the-sites reactivity in an enzyme, thymidylate synthase, involves a relay of changes between subunits
-
Anderson A.C., O'Neil R.H., DeLano W.L., Stroud R.M. The structural mechanism for half-the-sites reactivity in an enzyme, thymidylate synthase, involves a relay of changes between subunits. Biochemistry. 38:1999;13829-13836.
-
(1999)
Biochemistry
, vol.38
, pp. 13829-13836
-
-
Anderson, A.C.1
O'Neil, R.H.2
Delano, W.L.3
Stroud, R.M.4
-
33
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
34
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., Olson A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19:1998;1639-1662.
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
35
-
-
0024278707
-
Properties of a defined mutant of Escherichia coli thymidylate synthase
-
Maley G.F., Maley F. Properties of a defined mutant of Escherichia coli thymidylate synthase. J. Biol. Chem. 263:1988;7620-7627.
-
(1988)
J. Biol. Chem.
, vol.263
, pp. 7620-7627
-
-
Maley, G.F.1
Maley, F.2
-
36
-
-
0026935998
-
Purification methods for recombinant Lactobacillus casei thymidylate synthase and mutants: A general, automated procedure
-
Kealey J.T., Santi D.V. Purification methods for recombinant Lactobacillus casei thymidylate synthase and mutants. a general, automated procedure Protein Expr. Purif. 4:1992;380-385.
-
(1992)
Protein Expr. Purif.
, vol.4
, pp. 380-385
-
-
Kealey, J.T.1
Santi, D.V.2
-
37
-
-
0026232320
-
Purification and characterization of recombinant Pneumocystis carinii thymidylate synthase
-
Santi D.V., Edman U., Minkin S., Greene P.J. Purification and characterization of recombinant Pneumocystis carinii thymidylate synthase. Protein Expr. Purif. 2:1991;350-354.
-
(1991)
Protein Expr. Purif.
, vol.2
, pp. 350-354
-
-
Santi, D.V.1
Edman, U.2
Minkin, S.3
Greene, P.J.4
-
38
-
-
0346279739
-
Isolation and expression of the Pneumocystis carinii thymidylate synthase gene
-
Edman U., Edman J.C., Lundgren B., Santi D.V. Isolation and expression of the Pneumocystis carinii thymidylate synthase gene. Proc. Natl. Acad. Sci. USA. 84:1989;6503-6507.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 6503-6507
-
-
Edman, U.1
Edman, J.C.2
Lundgren, B.3
Santi, D.V.4
-
39
-
-
0020118322
-
A convenient procedure for purification of thymidylate synthase from L1210 cells
-
Banerjee C.K., Bennett L.L. Jr., Brockman R.W., Santi B.P., Temple C. Jr. A convenient procedure for purification of thymidylate synthase from L1210 cells. Anal. Biochem. 121:1982;275-280.
-
(1982)
Anal. Biochem.
, vol.121
, pp. 275-280
-
-
Banerjee, C.K.1
Bennett, L.L.Jr.2
Brockman, R.W.3
Santi, B.P.4
Temple, C.Jr.5
-
40
-
-
0024290404
-
Heterologous expression of the bifunctional thymidylate synthase-dihydrofolate reductase from Leishmania major
-
Grumont R., Sirawaraporn W., Santi D.V. Heterologous expression of the bifunctional thymidylate synthase-dihydrofolate reductase from Leishmania major. Biochemistry. 27:1988;3776-3784.
-
(1988)
Biochemistry
, vol.27
, pp. 3776-3784
-
-
Grumont, R.1
Sirawaraporn, W.2
Santi, D.V.3
-
41
-
-
0020959710
-
Studies on transformation of Escherichia coli with plasmids
-
Hanahan D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:1983;557-580.
-
(1983)
J. Mol. Biol.
, vol.166
, pp. 557-580
-
-
Hanahan, D.1
-
42
-
-
0022518273
-
Kinetics and mechanism of interaction of 10-propargyl-5,8-dideazafolate with thymidylate synthase
-
Pogolotti A.L. Jr., Danenberg P.V., Santi D.V. Kinetics and mechanism of interaction of 10-propargyl-5,8-dideazafolate with thymidylate synthase. J. Med. Chem. 29:1986;478-482.
-
(1986)
J. Med. Chem.
, vol.29
, pp. 478-482
-
-
Pogolotti, A.L.Jr.1
Danenberg, P.V.2
Santi, D.V.3
-
45
-
-
0004268506
-
-
University of California, San Francisco
-
Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, T.E., III, Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., et al. (1999). AMBER 6. University of California, San Francisco.
-
(1999)
AMBER 6
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham, T.E.4
III Ross, W.S.5
Simmerling, C.L.6
Darden, T.A.7
Merz, K.M.8
Stanton, R.V.9
Cheng, A.L.10
-
46
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M. Jr., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.Jr.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
47
-
-
0025398721
-
Whatif: A molecular modeling and drug design program
-
Vriend G. Whatif. A molecular modeling and drug design program J. Mol. Graph. 8:1990;52-56.
-
(1990)
J. Mol. Graph.
, vol.8
, pp. 52-56
-
-
Vriend, G.1
|