-
1
-
-
46849089254
-
Recent developments in fragment-based drug discovery
-
M. Congreve Recent developments in fragment-based drug discovery J. Med. Chem. 51 2008 3661 3680
-
(2008)
J. Med. Chem.
, vol.51
, pp. 3661-3680
-
-
Congreve, M.1
-
2
-
-
0141726877
-
A 'rule of three' for fragment-based lead discovery?
-
M. Congreve A 'rule of three' for fragment-based lead discovery? Drug Discov. Today 8 2003 876 877
-
(2003)
Drug Discov. Today
, vol.8
, pp. 876-877
-
-
Congreve, M.1
-
3
-
-
16244388286
-
Virtual exploration of the small-molecule chemical universe below 160 Daltons
-
T. Fink Virtual exploration of the small-molecule chemical universe below 160 Daltons Angew. Chem. Int. Ed. Engl. 44 2005 1504 1508
-
(2005)
Angew. Chem. Int. Ed. Engl.
, vol.44
, pp. 1504-1508
-
-
Fink, T.1
-
4
-
-
13844312649
-
ZINC - A free database of commercially available compounds for virtual screening
-
J.J. Irwin, and B.K. Shoichet ZINC - a free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 45 2005 177 182
-
(2005)
J. Chem. Inf. Model.
, vol.45
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
5
-
-
56749182336
-
Fragment-based design of small molecule X-linked inhibitor of apoptosis protein inhibitors
-
J.W. Huang Fragment-based design of small molecule X-linked inhibitor of apoptosis protein inhibitors J. Med. Chem. 51 2008 7111 7118
-
(2008)
J. Med. Chem.
, vol.51
, pp. 7111-7118
-
-
Huang, J.W.1
-
6
-
-
33745199815
-
Virtual ligand screening: Strategies, perspectives and limitations
-
G. Klebe Virtual ligand screening: strategies, perspectives and limitations Drug Discov. Today 11 2006 580 594
-
(2006)
Drug Discov. Today
, vol.11
, pp. 580-594
-
-
Klebe, G.1
-
7
-
-
34249094150
-
Informatics and modeling challenges in fragment-based drug discovery
-
R.E. Hubbard Informatics and modeling challenges in fragment-based drug discovery Curr. Opin. Drug Discov. Dev. 10 2007 289 297
-
(2007)
Curr. Opin. Drug Discov. Dev.
, vol.10
, pp. 289-297
-
-
Hubbard, R.E.1
-
8
-
-
0025916872
-
Functionality maps of binding sites: A multiple copy simultaneous search method
-
A. Miranker, and M. Karplus Functionality maps of binding sites: a multiple copy simultaneous search method Proteins 11 1991 29 34
-
(1991)
Proteins
, vol.11
, pp. 29-34
-
-
Miranker, A.1
Karplus, M.2
-
9
-
-
78650734429
-
Fragment-docking to proteins with the Multi-copy Simultaneous Search Methodology
-
M.C. Stultz, and M. Karplus Fragment-docking to proteins with the Multi-copy Simultaneous Search Methodology W. Jahnke, D.A. Erlanson, Fragment-based Approaches in Drug Discovery 2006 Wiley-VCH 125 144
-
(2006)
Fragment-based Approaches in Drug Discovery
, pp. 125-144
-
-
Stultz, M.C.1
Karplus, M.2
-
10
-
-
33947658802
-
Identification of hot spots within druggable binding regions by computational solvent mapping of proteins
-
M.R. Landon Identification of hot spots within druggable binding regions by computational solvent mapping of proteins J. Med. Chem. 50 2007 1231 1240
-
(2007)
J. Med. Chem.
, vol.50
, pp. 1231-1240
-
-
Landon, M.R.1
-
11
-
-
68249132213
-
Computational fragment-based binding site identification by ligand competitive saturation
-
O. Guvench, and A.D. MacKerell Jr Computational fragment-based binding site identification by ligand competitive saturation PLoS Comput. Biol. 5 2009 e1000435
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. 1000435
-
-
Guvench, O.1
MacKerell, Jr.A.D.2
-
12
-
-
33244470695
-
Grand canonical Monte Carlo simulation of ligand-protein binding
-
M. Clark Grand canonical Monte Carlo simulation of ligand-protein binding J. Chem. Inf. Model. 46 2006 231 242
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 231-242
-
-
Clark, M.1
-
13
-
-
68149095775
-
Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics
-
D. Ekonomiuk Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics J. Med. Chem. 52 2009 4860 4868
-
(2009)
J. Med. Chem.
, vol.52
, pp. 4860-4868
-
-
Ekonomiuk, D.1
-
14
-
-
67651002876
-
Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
-
K. Loving Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation J. Comput. Aided Mol. Des. 2009
-
(2009)
J. Comput. Aided Mol. Des.
-
-
Loving, K.1
-
15
-
-
33947612966
-
Application of fragment screening by X-ray crystallography to beta-secretase
-
C.W. Murray Application of fragment screening by X-ray crystallography to beta-secretase J. Med. Chem. 50 2007 1116 1123
-
(2007)
J. Med. Chem.
, vol.50
, pp. 1116-1123
-
-
Murray, C.W.1
-
16
-
-
37849043411
-
Application of fragment-based lead generation to the discovery of novel, cyclic amidine beta-secretase inhibitors with nanomolar potency, cellular activity, and high ligand efficiency
-
P.D. Edwards Application of fragment-based lead generation to the discovery of novel, cyclic amidine beta-secretase inhibitors with nanomolar potency, cellular activity, and high ligand efficiency J. Med. Chem. 50 2007 5912 5925
-
(2007)
J. Med. Chem.
, vol.50
, pp. 5912-5925
-
-
Edwards, P.D.1
-
17
-
-
66149158600
-
Docking for fragment inhibitors of AmpC beta-lactamase
-
D.G. Teotico Docking for fragment inhibitors of AmpC beta-lactamase Proc. Natl. Acad. Sci. U. S. A. 106 2009 7455 7460
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 7455-7460
-
-
Teotico, D.G.1
-
18
-
-
65349195698
-
Molecular docking and ligand specificity in fragment-based inhibitor discovery
-
Y. Chen, and B.K. Shoichet Molecular docking and ligand specificity in fragment-based inhibitor discovery Nat. Chem. Biol. 5 2009 358 364
-
(2009)
Nat. Chem. Biol.
, vol.5
, pp. 358-364
-
-
Chen, Y.1
Shoichet, B.K.2
-
19
-
-
31344459599
-
In silico fragment-based discovery of DPP-IV S1 pocket binders
-
C. Rummey In silico fragment-based discovery of DPP-IV S1 pocket binders Bioorg. Med. Chem. Lett. 16 2006 1405 1409
-
(2006)
Bioorg. Med. Chem. Lett.
, vol.16
, pp. 1405-1409
-
-
Rummey, C.1
-
20
-
-
24944529911
-
Virtual screening against metalloenzymes for inhibitors and substrates
-
J.J. Irwin Virtual screening against metalloenzymes for inhibitors and substrates Biochemistry 44 2005 12316 12328
-
(2005)
Biochemistry
, vol.44
, pp. 12316-12328
-
-
Irwin, J.J.1
-
21
-
-
67650754042
-
One scaffold, three binding modes: Novel and selective pteridine reductase 1 inhibitors derived from fragment hits discovered by virtual screening
-
C.P. Mpamhanga One scaffold, three binding modes: novel and selective pteridine reductase 1 inhibitors derived from fragment hits discovered by virtual screening J. Med. Chem. 52 2009 4454 4465
-
(2009)
J. Med. Chem.
, vol.52
, pp. 4454-4465
-
-
Mpamhanga, C.P.1
-
22
-
-
77955330853
-
Virtual fragment screening for novel inhibitors of 6-phosphogluconate dehydrogenase
-
G.F. Ruda Virtual fragment screening for novel inhibitors of 6-phosphogluconate dehydrogenase Bioorg. Med. Chem. 18 2010 5056 5062
-
(2010)
Bioorg. Med. Chem.
, vol.18
, pp. 5056-5062
-
-
Ruda, G.F.1
-
23
-
-
41849136839
-
Novel prostaglandin D synthase inhibitors generated by fragment-based drug design
-
M. Hohwy Novel prostaglandin D synthase inhibitors generated by fragment-based drug design J. Med. Chem. 51 2008 2178 2186
-
(2008)
J. Med. Chem.
, vol.51
, pp. 2178-2186
-
-
Hohwy, M.1
-
24
-
-
67650997041
-
Virtual fragment screening: An exploration of various docking and scoring protocols for fragments using Glide
-
S. Kawatkar Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide J. Comput. Aided Mol. Des. 2009
-
(2009)
J. Comput. Aided Mol. Des.
-
-
Kawatkar, S.1
-
25
-
-
36248956723
-
The SeeDs approach: Integrating fragments into drug discovery
-
R.E. Hubbard The SeeDs approach: integrating fragments into drug discovery Curr. Top. Med. Chem. 7 2007 1568 1581
-
(2007)
Curr. Top. Med. Chem.
, vol.7
, pp. 1568-1581
-
-
Hubbard, R.E.1
-
26
-
-
77954036921
-
Virtual fragment docking by Glide: A validation study on 190 protein-fragment complexes
-
M. Sandor Virtual fragment docking by Glide: a validation study on 190 protein-fragment complexes J. Chem. Inf. Model 50 2010 1165 1172
-
(2010)
J. Chem. Inf. Model
, vol.50
, pp. 1165-1172
-
-
Sandor, M.1
-
27
-
-
67650951150
-
The multiple roles of computational chemistry in fragment-based drug design
-
R. Law The multiple roles of computational chemistry in fragment-based drug design J. Comput. Aided Mol. Des. 23 2009 459 473
-
(2009)
J. Comput. Aided Mol. Des.
, vol.23
, pp. 459-473
-
-
Law, R.1
-
28
-
-
49649114644
-
Fragment docking to S100 proteins reveals a wide diversity of weak interaction sites
-
Y. Arendt Fragment docking to S100 proteins reveals a wide diversity of weak interaction sites ChemMedChem 2 2007 1648 1654
-
(2007)
ChemMedChem
, vol.2
, pp. 1648-1654
-
-
Arendt, Y.1
-
29
-
-
76649089979
-
Library screening by fragment-based docking
-
D. Huang, and A. Caflisch Library screening by fragment-based docking J. Mol.Recognit. 23 2009 183 193
-
(2009)
J. Mol.Recognit.
, vol.23
, pp. 183-193
-
-
Huang, D.1
Caflisch, A.2
-
30
-
-
69549135452
-
Fragment-based computation of binding free energies by systematic sampling
-
M. Clark Fragment-based computation of binding free energies by systematic sampling J. Chem. Inf. Model. 49 2009 1901 1913
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1901-1913
-
-
Clark, M.1
-
31
-
-
52249108519
-
CONFIRM: Connecting fragments found in receptor molecules
-
D.C. Thompson CONFIRM: connecting fragments found in receptor molecules J. Comput. Aided Mol. Des. 22 2008 761 772
-
(2008)
J. Comput. Aided Mol. Des.
, vol.22
, pp. 761-772
-
-
Thompson, D.C.1
-
32
-
-
33748652464
-
FlexNovo: Structure-based searching in large fragment spaces
-
J. Degen, and M. Rarey FlexNovo: structure-based searching in large fragment spaces ChemMedChem 1 2006 854 868
-
(2006)
ChemMedChem
, vol.1
, pp. 854-868
-
-
Degen, J.1
Rarey, M.2
-
33
-
-
23844449940
-
Computer-based de novo design of drug-like molecules
-
G. Schneider, and U. Fechner Computer-based de novo design of drug-like molecules Nat. Rev. Drug Discov. 4 2005 649 663
-
(2005)
Nat. Rev. Drug Discov.
, vol.4
, pp. 649-663
-
-
Schneider, G.1
Fechner, U.2
-
34
-
-
77949345618
-
Computational approaches for fragment-based and de novo design
-
K. Loving Computational approaches for fragment-based and de novo design Curr. Top. Med. Chem. 10 2010 14 32
-
(2010)
Curr. Top. Med. Chem.
, vol.10
, pp. 14-32
-
-
Loving, K.1
-
35
-
-
0041989635
-
Conformational flexibility models for the receptor in structure based drug design
-
M.L. Teodoro, and L.E. Kavraki Conformational flexibility models for the receptor in structure based drug design Curr. Pharm. Des. 9 2003 1635 1648
-
(2003)
Curr. Pharm. Des.
, vol.9
, pp. 1635-1648
-
-
Teodoro, M.L.1
Kavraki, L.E.2
-
36
-
-
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
-
37
-
-
1842471241
-
Testing a flexible-receptor docking algorithm in a model binding site
-
B.Q. Wei Testing a flexible-receptor docking algorithm in a model binding site J. Mol. Biol. 337 2004 1161 1182
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 1161-1182
-
-
Wei, B.Q.1
-
38
-
-
52049093435
-
A poke in the eye: Inhibiting HIV-1 protease through its flap-recognition pocket
-
K.L. Damm A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket Biopolymers 89 2008 643 652
-
(2008)
Biopolymers
, vol.89
, pp. 643-652
-
-
Damm, K.L.1
-
39
-
-
40649101151
-
Rescoring docking hit lists for model cavity sites: Predictions and experimental testing
-
A.P. Graves Rescoring docking hit lists for model cavity sites: predictions and experimental testing J. Mol. Biol. 377 2008 914 934
-
(2008)
J. Mol. Biol.
, vol.377
, pp. 914-934
-
-
Graves, A.P.1
-
40
-
-
50249094315
-
Exploiting ordered waters in molecular docking
-
N. Huang, and B.K. Shoichet Exploiting ordered waters in molecular docking J. Med. Chem. 51 2008 4862 4865
-
(2008)
J. Med. Chem.
, vol.51
, pp. 4862-4865
-
-
Huang, N.1
Shoichet, B.K.2
-
41
-
-
0035044857
-
Experimental and computational mapping of the binding surface of a crystalline protein
-
A.C. English Experimental and computational mapping of the binding surface of a crystalline protein Protein Eng. 14 2001 47 59
-
(2001)
Protein Eng.
, vol.14
, pp. 47-59
-
-
English, A.C.1
-
42
-
-
33749242759
-
Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding
-
J. Tirado-Rives, and W.L. Jorgensen Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding J. Med. Chem. 49 2006 5880 5884
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5880-5884
-
-
Tirado-Rives, J.1
Jorgensen, W.L.2
-
43
-
-
67650149263
-
QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors
-
M.P. Gleeson, and D. Gleeson QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors J. Chem. Inf. Model. 49 2009 1437 1448
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1437-1448
-
-
Gleeson, M.P.1
Gleeson, D.2
-
44
-
-
33846933784
-
Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
-
G. Marcou, and D. Rognan Optimizing fragment and scaffold docking by use of molecular interaction fingerprints J. Chem. Inf. Model. 47 2007 195 207
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 195-207
-
-
Marcou, G.1
Rognan, D.2
-
45
-
-
68149170106
-
Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring
-
R. Friedman, and A. Caflisch Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring ChemMedChem 4 2009 1317 1326
-
(2009)
ChemMedChem
, vol.4
, pp. 1317-1326
-
-
Friedman, R.1
Caflisch, A.2
-
46
-
-
70449522914
-
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
-
S.E. Boyce Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site J. Mol. Biol. 394 2009 747 763
-
(2009)
J. Mol. Biol.
, vol.394
, pp. 747-763
-
-
Boyce, S.E.1
|