-
1
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: methods and applications
-
Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 2004;3:935-949.
-
(2004)
Nat Rev Drug Discov
, vol.3
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
2
-
-
67349261359
-
Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation
-
Jain A. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J Comput Aided Mol Des 2009;23:355-374.
-
(2009)
J Comput Aided Mol Des
, vol.23
, pp. 355-374
-
-
Jain, A.1
-
3
-
-
37249031360
-
Lessons in molecular recognition. II. Assessing and improving cross-docking accuracy
-
Sutherland JJ, Nandigam RK, Erickson JA, Vieth M. Lessons in molecular recognition. II. Assessing and improving cross-docking accuracy. J Chem Inf Model 2007;47:2293-2302.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 2293-2302
-
-
Sutherland, J.J.1
Nandigam, R.K.2
Erickson, J.A.3
Vieth, M.4
-
4
-
-
57549102789
-
Protein-ligand docking against non-native protein conformers
-
Verdonk ML, Mortenson PN, Hall RJ, Hartshorn MJ, Murray CW. Protein-ligand docking against non-native protein conformers. J Chem Inf Model 2008;48:2214-2225.
-
(2008)
J Chem Inf Model
, vol.48
, pp. 2214-2225
-
-
Verdonk, M.L.1
Mortenson, P.N.2
Hall, R.J.3
Hartshorn, M.J.4
Murray, C.W.5
-
5
-
-
84861118556
-
Outstanding challenges in protein-ligand docking and structure-based virtual screening
-
Waszkowycz B, Clark DE, Gancia E. Outstanding challenges in protein-ligand docking and structure-based virtual screening. Wiley Interdiscip Rev: Comput Mol Sci 2011;1:229-259.
-
(2011)
Wiley Interdiscip Rev: Comput Mol Sci
, vol.1
, pp. 229-259
-
-
Waszkowycz, B.1
Clark, D.E.2
Gancia, E.3
-
6
-
-
70350340728
-
The role of dynamic conformational ensembles in biomolecular recognition
-
Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009;5:789-796.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
7
-
-
77957231785
-
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
-
Csermely P, Palotai R, Nussinov R. Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. TIBS 2010;35;539-546.
-
(2010)
TIBS
, vol.35
, pp. 539-546
-
-
Csermely, P.1
Palotai, R.2
Nussinov, R.3
-
8
-
-
79958136745
-
A role for both conformational selection and induced fit in ligand binding by the LAO protein
-
Silva D-A, Bowman GR, Sosa-Peinado A, Huang X. A role for both conformational selection and induced fit in ligand binding by the LAO protein. PLoS Comput Biol 2011;7; e1002054.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Silva, D.-A.1
Bowman, G.R.2
Sosa-Peinado, A.3
Huang, X.4
-
9
-
-
60749137646
-
Toward accurate relative energy predictions of the bioactive conformation of drugs
-
Butler KT, Luque FJ, Barril X. Toward accurate relative energy predictions of the bioactive conformation of drugs. J Comput Chem 2009;30:601-610.
-
(2009)
J Comput Chem
, vol.30
, pp. 601-610
-
-
Butler, K.T.1
Luque, F.J.2
Barril, X.3
-
10
-
-
84893746990
-
-
Glide, version 5.7. New York, NY: Schrödinger, LLC
-
Glide, version 5.7. New York, NY: Schrödinger, LLC; 2011.
-
(2011)
-
-
-
11
-
-
0037102153
-
High resolution crystal structure of the human PDK1 catalytic domain defines the regulatory phosphopeptide docking site
-
Biondi RM, Komander D, Thomas CC, Lizcano JM, Deak M, Alessi DR, Aalten DMFv. High resolution crystal structure of the human PDK1 catalytic domain defines the regulatory phosphopeptide docking site. EMBO J 2002;21:4219-4228.
-
(2002)
EMBO J
, vol.21
, pp. 4219-4228
-
-
Biondi, R.M.1
Komander, D.2
Thomas, C.C.3
Lizcano, J.M.4
Deak, M.5
Alessi, D.R.6
Aalten, DMF.7
-
12
-
-
0142231577
-
Structural basis for UCN-01 (7-hydroxystaurosporine) specificity and PDK1 (3-phosphoinositide-dependent protein kinase-1) inhibition
-
Komander D, Kular GS, Bain J, Elliott M, Alessi DR, Aalten DMFv. Structural basis for UCN-01 (7-hydroxystaurosporine) specificity and PDK1 (3-phosphoinositide-dependent protein kinase-1) inhibition. Biochem J 2003;375:255-262.
-
(2003)
Biochem J
, vol.375
, pp. 255-262
-
-
Komander, D.1
Kular, G.S.2
Bain, J.3
Elliott, M.4
Alessi, D.R.5
Aalten, DMF.6
-
13
-
-
79952780435
-
Structure-based design of potent and selective 3-phosphoinositide-dependent kinase-1 (PDK1) inhibitors
-
Medina JR, Becker CJ, Blackledge CW, Duquenne C, Feng Y, Grant SW, Heerding D, Li WH, Miller WH, Romeril SP, Scherzer D, Shu A, Bobko MA, Chadderton AR, Dumble M, Gardiner CM, Gilbert S, Liu Q, Rabindran SK, Sudakin V, Xiang H, Brady PG, Campobasso N, Ward P, Axten JM. Structure-based design of potent and selective 3-phosphoinositide-dependent kinase-1 (PDK1) inhibitors. J Med Chem 2011;54:1871-1895.
-
(2011)
J Med Chem
, vol.54
, pp. 1871-1895
-
-
Medina, J.R.1
Becker, C.J.2
Blackledge, C.W.3
Duquenne, C.4
Feng, Y.5
Grant, S.W.6
Heerding, D.7
Li, W.H.8
Miller, W.H.9
Romeril, S.P.10
Scherzer, D.11
Shu, A.12
Bobko, M.A.13
Chadderton, A.R.14
Dumble, M.15
Gardiner, C.M.16
Gilbert, S.17
Liu, Q.18
Rabindran, S.K.19
Sudakin, V.20
Xiang, H.21
Brady, P.G.22
Campobasso, N.23
Ward, P.24
Axten, J.M.25
more..
-
14
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
-
(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
-
15
-
-
10744233962
-
Interactions of LY333531 and other bisindolyl maleimide inhibitors with PDK1
-
Komander D, Kular GS, Schuttelkopf AW, Deak M, Prakash K, Bain J, van Aalten DM. Interactions of LY333531 and other bisindolyl maleimide inhibitors with PDK1. Structure 2004;12:215-226.
-
(2004)
Structure
, vol.12
, pp. 215-226
-
-
Komander, D.1
Kular, G.S.2
Schuttelkopf, A.W.3
Deak, M.4
Prakash, K.5
Bain, J.6
van Aalten, D.M.7
-
16
-
-
21244435590
-
Novel small molecule inhibitors of 3-phosphoinositide-dependent kinase-1
-
Feldman RI, Wu JM, Polokoff MA, Kochanny MJ, Dinter H, Zhu D, Biroc SL, Alicke B, Bryant J, Yuan S, Buckman BO, Lentz D, Ferrer M, Whitlow M, Adler M, Finster S, Chang Z, Arnaiz DO. Novel small molecule inhibitors of 3-phosphoinositide-dependent kinase-1. J Biol Chem 2005;280:19867-19874.
-
(2005)
J Biol Chem
, vol.280
, pp. 19867-19874
-
-
Feldman, R.I.1
Wu, J.M.2
Polokoff, M.A.3
Kochanny, M.J.4
Dinter, H.5
Zhu, D.6
Biroc, S.L.7
Alicke, B.8
Bryant, J.9
Yuan, S.10
Buckman, B.O.11
Lentz, D.12
Ferrer, M.13
Whitlow, M.14
Adler, M.15
Finster, S.16
Chang, Z.17
Arnaiz, D.O.18
-
17
-
-
34250329460
-
Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 1: Design, synthesis and biological activity
-
Islam I, Bryant J, Chou Y-L, Kochanny MJ, Lee W, Phillips GB, Yu H, Adler M, Whitlow M, Ho E, Lentz D, Polokoff MA, Subramanyam B, Wu JM, Zhu D, Feldman RI, Arnaiz DO. Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 1: Design, synthesis and biological activity. Bioorg Med Chem Lett 2007;17:3814-3818.
-
(2007)
Bioorg Med Chem Lett
, vol.17
, pp. 3814-3818
-
-
Islam, I.1
Bryant, J.2
Chou, Y.-L.3
Kochanny, M.J.4
Lee, W.5
Phillips, G.B.6
Yu, H.7
Adler, M.8
Whitlow, M.9
Ho, E.10
Lentz, D.11
Polokoff, M.A.12
Subramanyam, B.13
Wu, J.M.14
Zhu, D.15
Feldman, R.I.16
Arnaiz, D.O.17
-
18
-
-
34250322969
-
Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 2: Optimization of BX-517
-
Islam I, Brown G, Bryant J, Hrvatin P, Kochanny MJ, Phillips GB, Yuan S, Adler M, Whitlow M, Lentz D, Polokoff MA, Wu J, Shen J, Walters J, Ho E, Subramanyam B, Zhu D, Feldman RI, Arnaiz DO. Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 2: Optimization of BX-517. Bioorg Med Chem Lett 2007;17:3819-3825.
-
(2007)
Bioorg Med Chem Lett
, vol.17
, pp. 3819-3825
-
-
Islam, I.1
Brown, G.2
Bryant, J.3
Hrvatin, P.4
Kochanny, M.J.5
Phillips, G.B.6
Yuan, S.7
Adler, M.8
Whitlow, M.9
Lentz, D.10
Polokoff, M.A.11
Wu, J.12
Shen, J.13
Walters, J.14
Ho, E.15
Subramanyam, B.16
Zhu, D.17
Feldman, R.I.18
Arnaiz, D.O.19
-
19
-
-
36149000161
-
Discovery of dibenzo[c,f][2,7]naphthyridines as potent and selective 3-phosphoinositide-dependent kinase-1 inhibitors
-
Gopalsamy A, Shi M, Boschelli DH, Williamson R, Olland A, Hu Y, Krishnamurthy G, Han X, Arndt K, Guo B. Discovery of dibenzo[c, f][2, 7]naphthyridines as potent and selective 3-phosphoinositide-dependent kinase-1 inhibitors. J Med Chem 2007;50:5547-5549.
-
(2007)
J Med Chem
, vol.50
, pp. 5547-5549
-
-
Gopalsamy, A.1
Shi, M.2
Boschelli, D.H.3
Williamson, R.4
Olland, A.5
Hu, Y.6
Krishnamurthy, G.7
Han, X.8
Arndt, K.9
Guo, B.10
-
20
-
-
77953872158
-
Structure-based optimization of potent PDK1 inhibitors
-
Angiolini M, Banfi P, Casale E, Casuscelli F, Fiorelli C, Saccardo MB, Silvagni M, Zuccotto F. Structure-based optimization of potent PDK1 inhibitors. Bioorg Med Chem Lett 2010;20:4095-4099.
-
(2010)
Bioorg Med Chem Lett
, vol.20
, pp. 4095-4099
-
-
Angiolini, M.1
Banfi, P.2
Casale, E.3
Casuscelli, F.4
Fiorelli, C.5
Saccardo, M.B.6
Silvagni, M.7
Zuccotto, F.8
-
21
-
-
68349155556
-
Benzo[c][2,7]naphthyridines as inhibitors of PDK-1
-
Kim KH, Wissner A, Floyd MB, Fraser HL, Wang YD, Dushin RG, Hu Y, Olland A, Guo B, Arndt K. Benzo[c][2, 7]naphthyridines as inhibitors of PDK-1. Bioorg Med Chem Lett 2009;19:5225-5228.
-
(2009)
Bioorg Med Chem Lett
, vol.19
, pp. 5225-5228
-
-
Kim, K.H.1
Wissner, A.2
Floyd, M.B.3
Fraser, H.L.4
Wang, Y.D.5
Dushin, R.G.6
Hu, Y.7
Olland, A.8
Guo, B.9
Arndt, K.10
-
22
-
-
77349085513
-
The identification of 8,9-dimethoxy-5-(2-aminoalkoxy-pyridin-3-yl)-benzo[c][2,7] naphthyridin-4-ylamines as potent inhibitors of 3-phosphoinositide-dependent kinase-1 (PDK-1)
-
Nittoli T, Dushin RG, Ingalls C, Cheung K, Floyd MB, Fraser H, Olland A, Hu Y, Grosu G, Han X, Arndt K, Guo B, Wissner A. The identification of 8, 9-dimethoxy-5-(2-aminoalkoxy-pyridin-3-yl)-benzo[c][2, 7] naphthyridin-4-ylamines as potent inhibitors of 3-phosphoinositide-dependent kinase-1 (PDK-1). Eur J Med Chem 2010;45:1379-1386.
-
(2010)
Eur J Med Chem
, vol.45
, pp. 1379-1386
-
-
Nittoli, T.1
Dushin, R.G.2
Ingalls, C.3
Cheung, K.4
Floyd, M.B.5
Fraser, H.6
Olland, A.7
Hu, Y.8
Grosu, G.9
Han, X.10
Arndt, K.11
Guo, B.12
Wissner, A.13
-
23
-
-
79953181999
-
Genetic and pharmacological inhibition of PDK1 in cancer cells: characterization of a selective allosteric kinase inhibitor
-
Nagashima K, Shumway SD, Sathyanarayanan S, Chen AH, Dolinski B, Xu Y, Keilhack H, Nguyen T, Wiznerowicz M, Li L, Lutterbach BA, Chi A, Paweletz C, Allison T, Yan Y, Munshi SK, Klippel A, Kraus M, Bobkova EV, Deshmukh S, Xu Z, Mueller U, Szewczak AA, Pan BS, Richon V, Pollock R, Blume-Jensen P, Northrup A, Andersen JN. Genetic and pharmacological inhibition of PDK1 in cancer cells: characterization of a selective allosteric kinase inhibitor. J Biol Chem 2011;286:6433-6448.
-
(2011)
J Biol Chem
, vol.286
, pp. 6433-6448
-
-
Nagashima, K.1
Shumway, S.D.2
Sathyanarayanan, S.3
Chen, A.H.4
Dolinski, B.5
Xu, Y.6
Keilhack, H.7
Nguyen, T.8
Wiznerowicz, M.9
Li, L.10
Lutterbach, B.A.11
Chi, A.12
Paweletz, C.13
Allison, T.14
Yan, Y.15
Munshi, S.K.16
Klippel, A.17
Kraus, M.18
Bobkova, E.V.19
Deshmukh, S.20
Xu, Z.21
Mueller, U.22
Szewczak, A.A.23
Pan, B.S.24
Richon, V.25
Pollock, R.26
Blume-Jensen, P.27
Northrup, A.28
Andersen, J.N.29
more..
-
24
-
-
79955038588
-
Turning a protein kinase on or off from a single allosteric site via disulfide trapping
-
Sadowsky JD, Burlingame MA, Wolan DW, McClendon CL, Jacobson MP, Wells JA. Turning a protein kinase on or off from a single allosteric site via disulfide trapping. Proc Natl Acad Sci USA 2011;108:6056-6061.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 6056-6061
-
-
Sadowsky, J.D.1
Burlingame, M.A.2
Wolan, D.W.3
McClendon, C.L.4
Jacobson, M.P.5
Wells, J.A.6
-
25
-
-
79959776222
-
Rapid preparation of triazolyl substituted NH-heterocyclic kinase inhibitors via one-pot Sonogashira coupling-TMS-deprotection-CuAAC sequence
-
Merkul E, Klukas F, Dorsch D, Grädler U, Greiner HE, Müller TJ. Rapid preparation of triazolyl substituted NH-heterocyclic kinase inhibitors via one-pot Sonogashira coupling-TMS-deprotection-CuAAC sequence. Org Biomol Chem 2011;9:5129-5136.
-
(2011)
Org Biomol Chem
, vol.9
, pp. 5129-5136
-
-
Merkul, E.1
Klukas, F.2
Dorsch, D.3
Grädler, U.4
Greiner, H.E.5
Müller, T.J.6
-
26
-
-
84055217593
-
Discovery of novel, potent, and selective inhibitors of 3-phosphoinositide-dependent kinase (PDK1)
-
Murphy ST, Alton G, Bailey S, Baxi SM, Burke BJ, Chappie TA, Ermolieff J, Ferre R, Greasley S, Hickey M, Humphrey J, Kablaoui N, Kath J, Kazmirski S, Kraus M, Kupchinsky S, Li J, Lingardo L, Marx MA, Richter D, Tanis SP, Tran K, Vernier W, Xie Z, Yin MJ, Yu XH. Discovery of novel, potent, and selective inhibitors of 3-phosphoinositide-dependent kinase (PDK1). J Med Chem 2011;54:8490-8500.
-
(2011)
J Med Chem
, vol.54
, pp. 8490-8500
-
-
Murphy, S.T.1
Alton, G.2
Bailey, S.3
Baxi, S.M.4
Burke, B.J.5
Chappie, T.A.6
Ermolieff, J.7
Ferre, R.8
Greasley, S.9
Hickey, M.10
Humphrey, J.11
Kablaoui, N.12
Kath, J.13
Kazmirski, S.14
Kraus, M.15
Kupchinsky, S.16
Li, J.17
Lingardo, L.18
Marx, M.A.19
Richter, D.20
Tanis, S.P.21
Tran, K.22
Vernier, W.23
Xie, Z.24
Yin, M.J.25
Yu, X.H.26
more..
-
27
-
-
80051799613
-
Novel isoquinolone PDK1 inhibitors discovered through fragment-based lead discovery
-
Johnson MC, Hu Q, Lingardo L, Ferre RA, Greasley S, Yan J, Kath J, Chen P, Ermolieff J, Alton G. Novel isoquinolone PDK1 inhibitors discovered through fragment-based lead discovery. J Comput -Aided Mol Des 2011;25:689-698.
-
(2011)
J Comput -Aided Mol Des
, vol.25
, pp. 689-698
-
-
Johnson, M.C.1
Hu, Q.2
Lingardo, L.3
Ferre, R.A.4
Greasley, S.5
Yan, J.6
Kath, J.7
Chen, P.8
Ermolieff, J.9
Alton, G.10
-
28
-
-
84893809036
-
-
LigPrep, version 2.5. New York, NY: Schrödinger, LLC
-
LigPrep, version 2.5. New York, NY: Schrödinger, LLC; 2011.
-
(2011)
-
-
-
29
-
-
0043162336
-
An internal-coordinate Monte Carlo method for searching conformational space
-
Chang G, Guida WC, Still WC. An internal-coordinate Monte Carlo method for searching conformational space. J Am Chem Soc 1989;111:4379-4386.
-
(1989)
J Am Chem Soc
, vol.111
, pp. 4379-4386
-
-
Chang, G.1
Guida, W.C.2
Still, W.C.3
-
30
-
-
84893741179
-
-
MacroModel, version 9.9. New York, NY; Schrödinger, LLC
-
MacroModel, version 9.9. New York, NY; Schrödinger, LLC; 2011.
-
(2011)
-
-
-
31
-
-
0344778061
-
Semi-analytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semi-analytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990;112:6127-6129.
-
(1990)
J Am Chem Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
32
-
-
0001903222
-
Note on the convergence of the conjugate gradient methods. (Note sur la convergence de méthodes de directions conjuguées)
-
Polak E, Ribière G. Note on the convergence of the conjugate gradient methods. (Note sur la convergence de méthodes de directions conjuguées). Rev Franç Inform Rech Opér 1969;3:35-43.
-
(1969)
Rev Franç Inform Rech Opér
, vol.3
, pp. 35-43
-
-
Polak, E.1
Ribière, G.2
-
33
-
-
84893802391
-
-
Schrödinger Suite 2011 Protein Preparation Wizard; Epik version 2.2, Impact version 5.7, Prime version 3.0, New York, NY: Schrödinger, LLC
-
Schrödinger Suite 2011 Protein Preparation Wizard; Epik version 2.2, Impact version 5.7, Prime version 3.0, New York, NY: Schrödinger, LLC; 2011.
-
(2011)
-
-
-
34
-
-
2342586724
-
Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding
-
Perola E, Charifson PS. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J Med Chem 2004;47:2499-2510.
-
(2004)
J Med Chem
, vol.47
, pp. 2499-2510
-
-
Perola, E.1
Charifson, P.S.2
-
35
-
-
0037013143
-
The conformational plasticity of protein kinases
-
Huse M, Kuriyan J. The conformational plasticity of protein kinases. Cell 2002;109:275-282.
-
(2002)
Cell
, vol.109
, pp. 275-282
-
-
Huse, M.1
Kuriyan, J.2
-
36
-
-
33749242759
-
Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding
-
Tirado-Rives J, Jorgensen WL. Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding. J Med Chem 2006;49:5880-5884.
-
(2006)
J Med Chem
, vol.49
, pp. 5880-5884
-
-
Tirado-Rives, J.1
Jorgensen, W.L.2
-
37
-
-
0031075977
-
Solvation free energies of peptides: comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation
-
Edinger SR, Cortis C, Shenkin PS, Friesner RA. Solvation free energies of peptides: comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation. J Phys Chem B 1997;101:1190-1197.
-
(1997)
J Phys Chem B
, vol.101
, pp. 1190-1197
-
-
Edinger, S.R.1
Cortis, C.2
Shenkin, P.S.3
Friesner, R.A.4
-
38
-
-
0036606483
-
Principles of docking: an overview of search algorithms and a guide to scoring functions
-
Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins: Struct Funct Bioinf 2002;47:409-443.
-
(2002)
Proteins: Struct Funct Bioinf
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
39
-
-
0035765452
-
Small molecule docking and scoring
-
Lipkowitz KB, Boyd DB, editors. New York: Wiley.
-
Muegge I, Rarey M. Small molecule docking and scoring. In: Lipkowitz KB, Boyd DB, editors. Reviews in computational chemistry. New York: Wiley; 2001. pp 1-60.
-
(2001)
Reviews in computational chemistry
, pp. 1-60
-
-
Muegge, I.1
Rarey, M.2
-
40
-
-
0035416126
-
High-throughput docking for lead generation
-
Abagyan R, Totrov M. High-throughput docking for lead generation. Curr Opin Chem Biol 2001;5:375-382.
-
(2001)
Curr Opin Chem Biol
, vol.5
, pp. 375-382
-
-
Abagyan, R.1
Totrov, M.2
-
42
-
-
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 2000;295:337-356.
-
(2000)
J Mol Biol
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
43
-
-
84863097556
-
The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures
-
Liebeschuetz J, Hennemann J, Olsson T, Groom C. The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures. J Comput Aided Mol Des 2012;26:169-183.
-
(2012)
J Comput Aided Mol Des
, vol.26
, pp. 169-183
-
-
Liebeschuetz, J.1
Hennemann, J.2
Olsson, T.3
Groom, C.4
-
44
-
-
77951987154
-
ConfGen: a conformational search method for efficient generation of bioactive conformers
-
Watts KS, Dalal P, Murphy RB, Sherman W, Friesner RA, Shelley JC. ConfGen: a conformational search method for efficient generation of bioactive conformers. J Chem Inf Model 2010;50:534-546.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 534-546
-
-
Watts, K.S.1
Dalal, P.2
Murphy, R.B.3
Sherman, W.4
Friesner, R.A.5
Shelley, J.C.6
-
47
-
-
52249114682
-
Limitations and lessons in the use of X-ray structural information in drug design
-
Davis AM, St-Gallay SA, Kleywegt GJ. Limitations and lessons in the use of X-ray structural information in drug design. Drug Discov Today 2008;13:831-841.
-
(2008)
Drug Discov Today
, vol.13
, pp. 831-841
-
-
Davis, A.M.1
St-Gallay, S.A.2
Kleywegt, G.J.3
-
48
-
-
0038336897
-
Application and limitations of X-ray crystallographic data in structure-based ligand and drug design
-
Davis AM, Teague SJ, Kleywegt GJ. Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew Chem Int Ed 2003;42:2718-2736.
-
(2003)
Angew Chem Int Ed
, vol.42
, pp. 2718-2736
-
-
Davis, A.M.1
Teague, S.J.2
Kleywegt, G.J.3
-
49
-
-
84859191545
-
PDB ligand conformational energies calculated quantum-mechanically
-
Sitzmann M, Weidlich IE, Filippov IV, Liao C, Peach ML, Ihlenfeldt W-D, Karki RG, Borodina YV, Cachau RE, Nicklaus MC. PDB ligand conformational energies calculated quantum-mechanically. J Chem Inf Model 2012;52:739-756.
-
(2012)
J Chem Inf Model
, vol.52
, pp. 739-756
-
-
Sitzmann, M.1
Weidlich, I.E.2
Filippov, I.V.3
Liao, C.4
Peach, M.L.5
Ihlenfeldt, W.-D.6
Karki, R.G.7
Borodina, Y.V.8
Cachau, R.E.9
Nicklaus, M.C.10
-
50
-
-
35748934487
-
The influence of drug-like concepts on decision-making in medicinal chemistry
-
Leeson PD, Springthorpe B. The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discov 2007;6:881-890.
-
(2007)
Nat Rev Drug Discov
, vol.6
, pp. 881-890
-
-
Leeson, P.D.1
Springthorpe, B.2
-
51
-
-
34447548576
-
Ligand efficiency indices for effective drug discovery
-
Abad-Zapatero C. Ligand efficiency indices for effective drug discovery. Expert Opin Drug Discov 2007;2:469-488.
-
(2007)
Expert Opin Drug Discov
, vol.2
, pp. 469-488
-
-
Abad-Zapatero, C.1
|