-
1
-
-
33845903833
-
Drugs for bad bugs: Confronting the challenges of antibacterial discovery
-
Payne, D. J.; Gwynn, M. N.; Holmes, D. J.; Pompliano, D. L. Drugs for bad bugs: confronting the challenges of antibacterial discovery Nat. Rev. Drug Discovery 2007, 6, 29-40
-
(2007)
Nat. Rev. Drug Discovery
, vol.6
, pp. 29-40
-
-
Payne, D.J.1
Gwynn, M.N.2
Holmes, D.J.3
Pompliano, D.L.4
-
2
-
-
33947588563
-
Healthcare-associated infection and antimicrobial resistance: Moving beyond description to prevention
-
Zell, B. L.; Goldmann, D. A. Healthcare-associated infection and antimicrobial resistance: moving beyond description to prevention Infect. Control Hosp. Epidemiol. 2007, 28, 261-264
-
(2007)
Infect. Control Hosp. Epidemiol.
, vol.28
, pp. 261-264
-
-
Zell, B.L.1
Goldmann, D.A.2
-
3
-
-
57749107808
-
Bad bugs, no drugs: No ESKAPE! An update from the Infectious Diseases Society of America
-
Boucher, H. W.; Talbot, G. H.; Bradley, J. S.; Edwards, J. E.; Gilbert, D.; Rice, L. B.; Scheld, M.; Spellberg, B.; Bartlett, J. Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America Clin. Infect. Dis. 2009, 48, 1-12
-
(2009)
Clin. Infect. Dis.
, vol.48
, pp. 1-12
-
-
Boucher, H.W.1
Talbot, G.H.2
Bradley, J.S.3
Edwards, J.E.4
Gilbert, D.5
Rice, L.B.6
Scheld, M.7
Spellberg, B.8
Bartlett, J.9
-
4
-
-
48949098886
-
Purine salvage pathways in the intraerythrocytic malaria parasite Plasmodium falciparum
-
Downie, M. J.; Kirk, K.; Mamoun, C. B. Purine salvage pathways in the intraerythrocytic malaria parasite Plasmodium falciparum Eukaryotic Cell 2008, 7, 1231-1237
-
(2008)
Eukaryotic Cell
, vol.7
, pp. 1231-1237
-
-
Downie, M.J.1
Kirk, K.2
Mamoun, C.B.3
-
5
-
-
0023398205
-
Effect of different purine auxotrophic mutations on mouse-virulence of a Vi-positive strain of Salmonella dublin and of two strains of Salmonella typhimurium
-
McFarland, W. C.; Stocker, B. A. Effect of different purine auxotrophic mutations on mouse-virulence of a Vi-positive strain of Salmonella dublin and of two strains of Salmonella typhimurium Microb. Pathog. 1987, 3, 129-141
-
(1987)
Microb. Pathog.
, vol.3
, pp. 129-141
-
-
McFarland, W.C.1
Stocker, B.A.2
-
6
-
-
40349098615
-
Nucleotide biosynthesis is critical for growth of bacteria in human blood
-
Samant, S.; Lee, H.; Ghassemi, M.; Chen, J.; Cook, J. L.; Mankin, A. S.; Neyfakh, A. A. Nucleotide biosynthesis is critical for growth of bacteria in human blood PLoS Pathog. 2008, 4, e37
-
(2008)
PLoS Pathog.
, vol.4
, pp. 37
-
-
Samant, S.1
Lee, H.2
Ghassemi, M.3
Chen, J.4
Cook, J.L.5
Mankin, A.S.6
Neyfakh, A.A.7
-
7
-
-
0014329676
-
The growth of purine mutants of Bacillus anthracis in the body of the mouse
-
Ivanovics, G.; Marjai, E.; Dobozy, A. The growth of purine mutants of Bacillus anthracis in the body of the mouse J. Gen. Microbiol. 1968, 53, 147-162
-
(1968)
J. Gen. Microbiol.
, vol.53
, pp. 147-162
-
-
Ivanovics, G.1
Marjai, E.2
Dobozy, A.3
-
8
-
-
0021268201
-
Growth in mouse peritoneal macrophages of Yersinia pestis lacking established virulence determinants
-
Straley, S. C.; Harmon, P. A. Growth in mouse peritoneal macrophages of Yersinia pestis lacking established virulence determinants Infect. Immun. 1984, 45, 649-654
-
(1984)
Infect. Immun.
, vol.45
, pp. 649-654
-
-
Straley, S.C.1
Harmon, P.A.2
-
9
-
-
0030609131
-
Identification of Staphylococcus aureus virulence genes in a murine model of bacteraemia using signature-tagged mutagenesis
-
Mei, J. M.; Nourbakhsh, F.; Ford, C. W.; Holden, D. W. Identification of Staphylococcus aureus virulence genes in a murine model of bacteraemia using signature-tagged mutagenesis Mol. Microbiol. 1997, 26, 399-407
-
(1997)
Mol. Microbiol.
, vol.26
, pp. 399-407
-
-
Mei, J.M.1
Nourbakhsh, F.2
Ford, C.W.3
Holden, D.W.4
-
10
-
-
0031740873
-
Large-scale identification of virulence genes from Streptococcus pneumoniae
-
Polissi, A.; Pontiggia, A.; Feger, G.; Altieri, M.; Mottl, H.; Ferrari, L.; Simon, D. Large-scale identification of virulence genes from Streptococcus pneumoniae Infect. Immun. 1998, 66, 5620-5629
-
(1998)
Infect. Immun.
, vol.66
, pp. 5620-5629
-
-
Polissi, A.1
Pontiggia, A.2
Feger, G.3
Altieri, M.4
Mottl, H.5
Ferrari, L.6
Simon, D.7
-
11
-
-
0025330317
-
Genes of the Escherichia coli pur regulon are negatively controlled by a repressor-operator interaction
-
He, B.; Shiau, A.; Choi, K. Y.; Zalkin, H.; Smith, J. M. Genes of the Escherichia coli pur regulon are negatively controlled by a repressor-operator interaction J. Bacteriol. 1990, 172, 4555-4562
-
(1990)
J. Bacteriol.
, vol.172
, pp. 4555-4562
-
-
He, B.1
Shiau, A.2
Choi, K.Y.3
Zalkin, H.4
Smith, J.M.5
-
12
-
-
0025990055
-
De novo purine nucleotide biosynthesis: Cloning, sequencing and expression of a chicken PurH cDNA encoding 5-aminoimidazole-4-carboxamide- ribonucleotide transformylase-IMP cyclohydrolase
-
Ni, L.; Guan, K.; Zalkin, H.; Dixon, J. E. De novo purine nucleotide biosynthesis: cloning, sequencing and expression of a chicken PurH cDNA encoding 5-aminoimidazole-4-carboxamide-ribonucleotide transformylase-IMP cyclohydrolase Gene 1991, 106, 197-205
-
(1991)
Gene
, vol.106
, pp. 197-205
-
-
Ni, L.1
Guan, K.2
Zalkin, H.3
Dixon, J.E.4
-
13
-
-
33947230529
-
N5-CAIR mutase: Role of a CO2 binding site and substrate movement in catalysis
-
Hoskins, A. A.; Morar, M.; Kappock, T. J.; Mathews, I. I.; Zaugg, J. B.; Barder, T. E.; Peng, P.; Okamoto, A.; Ealick, S. E.; Stubbe, J. N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis Biochemistry 2007, 46, 2842-2855
-
(2007)
Biochemistry
, vol.46
, pp. 2842-2855
-
-
Hoskins, A.A.1
Morar, M.2
Kappock, T.J.3
Mathews, I.I.4
Zaugg, J.B.5
Barder, T.E.6
Peng, P.7
Okamoto, A.8
Ealick, S.E.9
Stubbe, J.10
-
14
-
-
0029836110
-
Large-scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection
-
Wang, J.; Mushegian, A.; Lory, S.; Jin, S. Large-scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 10434-10439
-
(1996)
Proc. Natl. Acad. Sci. U. S. A.
, vol.93
, pp. 10434-10439
-
-
Wang, J.1
Mushegian, A.2
Lory, S.3
Jin, S.4
-
15
-
-
0027945405
-
Reactions catalyzed by 5-aminoimidazole ribonucleotide carboxylases from Escherichia coli and Gallus gallus: A case for divergent catalytic mechanisms
-
Firestine, S. M.; Poon, S. W.; Mueller, E. J.; Stubbe, J.; Davisson, V. J. Reactions catalyzed by 5-aminoimidazole ribonucleotide carboxylases from Escherichia coli and Gallus gallus: a case for divergent catalytic mechanisms Biochemistry 1994, 33, 11927-11934
-
(1994)
Biochemistry
, vol.33
, pp. 11927-11934
-
-
Firestine, S.M.1
Poon, S.W.2
Mueller, E.J.3
Stubbe, J.4
Davisson, V.J.5
-
16
-
-
0033571625
-
Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway
-
Mathews, I. I.; Kappock, T. J.; Stubbe, J.; Ealick, S. E. Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway Structure 1999, 7, 1395-1406
-
(1999)
Structure
, vol.7
, pp. 1395-1406
-
-
Mathews, I.I.1
Kappock, T.J.2
Stubbe, J.3
Ealick, S.E.4
-
17
-
-
79960244405
-
Predicting fragment binding poses using a combined MCSS MM-GBSA approach
-
Haider, M. K.; Bertrand, H. O.; Hubbard, R. E. Predicting fragment binding poses using a combined MCSS MM-GBSA approach J. Chem. Inf. Model. 2011, 51, 1092-1105
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 1092-1105
-
-
Haider, M.K.1
Bertrand, H.O.2
Hubbard, R.E.3
-
18
-
-
84868526878
-
Discovery and optimization of a novel spiropyrrolidine inhibitor of beta-secretase (BACE1) through fragment-based drug design
-
Efremov, I. V.; Vajdos, F. F.; Borzilleri, K. A.; Capetta, S.; Chen, H.; Dorff, P. H.; Dutra, J. K.; Goldstein, S. W.; Mansour, M.; McColl, A.; Noell, S.; Oborski, C. E.; O'Connell, T. N.; O'Sullivan, T. J.; Pandit, J.; Wang, H.; Wei, B.; Withka, J. M. Discovery and optimization of a novel spiropyrrolidine inhibitor of beta-secretase (BACE1) through fragment-based drug design J. Med. Chem. 2012, 55, 9069-9088
-
(2012)
J. Med. Chem.
, vol.55
, pp. 9069-9088
-
-
Efremov, I.V.1
Vajdos, F.F.2
Borzilleri, K.A.3
Capetta, S.4
Chen, H.5
Dorff, P.H.6
Dutra, J.K.7
Goldstein, S.W.8
Mansour, M.9
McColl, A.10
Noell, S.11
Oborski, C.E.12
O'Connell, T.N.13
O'Sullivan, T.J.14
Pandit, J.15
Wang, H.16
Wei, B.17
Withka, J.M.18
-
19
-
-
84856399470
-
Fragment-based discovery of bromodomain inhibitors part 2: Optimization of phenylisoxazole sulfonamides
-
Bamborough, P.; Diallo, H.; Goodacre, J. D.; Gordon, L.; Lewis, A.; Seal, J. T.; Wilson, D. M.; Woodrow, M. D.; Chung, C. W. Fragment-based discovery of bromodomain inhibitors part 2: optimization of phenylisoxazole sulfonamides J. Med. Chem. 2012, 55, 587-596
-
(2012)
J. Med. Chem.
, vol.55
, pp. 587-596
-
-
Bamborough, P.1
Diallo, H.2
Goodacre, J.D.3
Gordon, L.4
Lewis, A.5
Seal, J.T.6
Wilson, D.M.7
Woodrow, M.D.8
Chung, C.W.9
-
20
-
-
80051860673
-
From fragment screening to in vivo efficacy: Optimization of a series of 2-aminoquinolines as potent inhibitors of beta-site amyloid precursor protein cleaving enzyme 1 (BACE1)
-
Cheng, Y.; Judd, T. C.; Bartberger, M. D.; Brown, J.; Chen, K.; Fremeau, R. T.; Hickman, D.; Hitchcock, S. A.; Jordan, B.; Li, V.; Lopez, P.; Louie, S. W.; Luo, Y.; Michelsen, K.; Nixey, T.; Powers, T. S.; Rattan, C.; Sickmier, E. A.; St Jean, D. J.; Wahl, R. C.; Wen, P. H.; Wood, S. From fragment screening to in vivo efficacy: optimization of a series of 2-aminoquinolines as potent inhibitors of beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) J. Med. Chem. 2011, 54, 5836-5857
-
(2011)
J. Med. Chem.
, vol.54
, pp. 5836-5857
-
-
Cheng, Y.1
Judd, T.C.2
Bartberger, M.D.3
Brown, J.4
Chen, K.5
Fremeau, R.T.6
Hickman, D.7
Hitchcock, S.A.8
Jordan, B.9
Li, V.10
Lopez, P.11
Louie, S.W.12
Luo, Y.13
Michelsen, K.14
Nixey, T.15
Powers, T.S.16
Rattan, C.17
Sickmier, E.A.18
St Jean, D.J.19
Wahl, R.C.20
Wen, P.H.21
Wood, S.22
more..
-
21
-
-
77955863827
-
Fragment-based drug discovery applied to Hsp90. Discovery of two lead series with high ligand efficiency
-
Murray, C. W.; Carr, M. G.; Callaghan, O.; Chessari, G.; Congreve, M.; Cowan, S.; Coyle, J. E.; Downham, R.; Figueroa, E.; Frederickson, M.; Graham, B.; McMenamin, R.; O'Brien, M. A.; Patel, S.; Phillips, T. R.; Williams, G.; Woodhead, A. J.; Woolford, A. J. Fragment-based drug discovery applied to Hsp90. Discovery of two lead series with high ligand efficiency J. Med. Chem. 2010, 53, 5942-5955
-
(2010)
J. Med. Chem.
, vol.53
, pp. 5942-5955
-
-
Murray, C.W.1
Carr, M.G.2
Callaghan, O.3
Chessari, G.4
Congreve, M.5
Cowan, S.6
Coyle, J.E.7
Downham, R.8
Figueroa, E.9
Frederickson, M.10
Graham, B.11
McMenamin, R.12
O'Brien, M.A.13
Patel, S.14
Phillips, T.R.15
Williams, G.16
Woodhead, A.J.17
Woolford, A.J.18
-
22
-
-
77953092035
-
Fragment-based lead discovery: Screening and optimizing fragments for thermolysin inhibition
-
Englert, L.; Silber, K.; Steuber, H.; Brass, S.; Over, B.; Gerber, H. D.; Heine, A.; Diederich, W. E.; Klebe, G. Fragment-based lead discovery: screening and optimizing fragments for thermolysin inhibition ChemMedChem 2010, 5, 930-940
-
(2010)
ChemMedChem
, vol.5
, pp. 930-940
-
-
Englert, L.1
Silber, K.2
Steuber, H.3
Brass, S.4
Over, B.5
Gerber, H.D.6
Heine, A.7
Diederich, W.E.8
Klebe, G.9
-
23
-
-
84862869077
-
Fragment-based approaches in drug discovery and chemical biology
-
Scott, D. E.; Coyne, A. G.; Hudson, S. A.; Abell, C. Fragment-based approaches in drug discovery and chemical biology Biochemistry 2012, 51, 4990-5003
-
(2012)
Biochemistry
, vol.51
, pp. 4990-5003
-
-
Scott, D.E.1
Coyne, A.G.2
Hudson, S.A.3
Abell, C.4
-
24
-
-
84875472128
-
-
Suite 2012: LigPrep, version 2.5, version 2.5; Schrödinger, LLC: New York, NY
-
Suite 2012: LigPrep, version 2.5, version 2.5; Schrödinger, LLC: New York, NY, 2012.
-
(2012)
-
-
-
25
-
-
37749011993
-
Epik: A software program for pK(a) prediction and protonation state generation for drug-like molecules
-
Shelley, J. C.; Cholleti, A.; Frye, L. L.; Greenwood, J. R.; Timlin, M. R.; Uchimaya, M. Epik: a software program for pK(a) prediction and protonation state generation for drug-like molecules J. Comput.-Aided Mol. Des. 2007, 21, 681-691
-
(2007)
J. Comput.-Aided Mol. Des.
, vol.21
, pp. 681-691
-
-
Shelley, J.C.1
Cholleti, A.2
Frye, L.L.3
Greenwood, J.R.4
Timlin, M.R.5
Uchimaya, M.6
-
26
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 1997, 267, 727-748
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
27
-
-
84875476181
-
-
AMBER 11; University of California: San Francisco
-
Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B. P.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER 11; University of California: San Francisco, 2010.
-
(2010)
-
-
Case, D.A.1
Darden, T.A.2
Cheatham Iii, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.10
Roberts, B.P.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossvary, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Cai, Q.24
Ye, X.25
Wang, J.26
Hsieh, M.-J.27
Cui, G.28
Roe, D.R.29
Mathews, D.H.30
Seetin, M.G.31
Sagui, C.32
Babin, V.33
Luchko, T.34
Gusarov, S.35
Kovalenko, A.36
Kollman, P.A.37
more..
-
28
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
29
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs J. Comput. Chem. 2005, 26, 1668-1688
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham Iii, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
30
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
31
-
-
33846823909
-
Particle mesh Ewald - An N.Log(N) method for Ewald sums in large systems
-
Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald-an N.Log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
32
-
-
33646940952
-
Numerical-integration of Cartesian equations of motion of a system with constraints - Molecular-dynamics of N-alkanes
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical-integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes J. Comput. Phys. 1977, 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
33
-
-
65249187243
-
MM-PBSA captures key role of intercalating water molecules at a protein-protein interface
-
Wong, S.; Amaro, R. E.; McCammon, J. A. MM-PBSA captures key role of intercalating water molecules at a protein-protein interface J. Chem. Theory Comput. 2009, 5, 422-429
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 422-429
-
-
Wong, S.1
Amaro, R.E.2
McCammon, J.A.3
-
34
-
-
84866167816
-
MMPBSA.py: An efficient program for end-state free energy calculations
-
Miller, B. R.; McGee, D. T.; Swails, J. M.; Homeyer, N.; Gohlke, H.; Roitberg, A. E. MMPBSA.py: An efficient program for end-state free energy calculations J. Chem. Theory Comput. 2012, 8, 3314-3321
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3314-3321
-
-
Miller, B.R.1
McGee, D.T.2
Swails, J.M.3
Homeyer, N.4
Gohlke, H.5
Roitberg, A.E.6
-
35
-
-
0034811498
-
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
-
Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA J. Am. Chem. Soc. 2001, 123, 5221-5230
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 5221-5230
-
-
Wang, J.1
Morin, P.2
Wang, W.3
Kollman, P.A.4
-
36
-
-
1942453243
-
Ligand efficiency: A useful metric for lead selection
-
Hopkins, A. L.; Groom, C. R.; Alex, A. Ligand efficiency: a useful metric for lead selection Drug Discovery Today 2004, 9, 430-431
-
(2004)
Drug Discovery Today
, vol.9
, pp. 430-431
-
-
Hopkins, A.L.1
Groom, C.R.2
Alex, A.3
-
37
-
-
79851483555
-
A practical use of ligand efficiency indices out of the fragment-based approach: Ligand efficiency-guided lead identification of soluble epoxide hydrolase inhibitors
-
Tanaka, D.; Tsuda, Y.; Shiyama, T.; Nishimura, T.; Chiyo, N.; Tominaga, Y.; Sawada, N.; Mimoto, T.; Kusunose, N. A practical use of ligand efficiency indices out of the fragment-based approach: ligand efficiency-guided lead identification of soluble epoxide hydrolase inhibitors J. Med. Chem. 2011, 54, 851-857
-
(2011)
J. Med. Chem.
, vol.54
, pp. 851-857
-
-
Tanaka, D.1
Tsuda, Y.2
Shiyama, T.3
Nishimura, T.4
Chiyo, N.5
Tominaga, Y.6
Sawada, N.7
Mimoto, T.8
Kusunose, N.9
-
38
-
-
77951992987
-
Ensemble docking into multiple crystallographically derived protein structures: An evaluation based on the statistical analysis of enrichments
-
Craig, I. R.; Essex, J. W.; Spiegel, K. Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments J. Chem. Inf. Model. 2010, 50, 511-524
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 511-524
-
-
Craig, I.R.1
Essex, J.W.2
Spiegel, K.3
-
39
-
-
27544451975
-
Crystal structure of PurE (BA0288) from Bacillus anthracis at 1.8 A resolution
-
Boyle, M. P.; Kalliomaa, A. K.; Levdikov, V.; Blagova, E.; Fogg, M. J.; Brannigan, J. A.; Wilson, K. S.; Wilkinson, A. J. Crystal structure of PurE (BA0288) from Bacillus anthracis at 1.8 A resolution Proteins 2005, 61, 674-676
-
(2005)
Proteins
, vol.61
, pp. 674-676
-
-
Boyle, M.P.1
Kalliomaa, A.K.2
Levdikov, V.3
Blagova, E.4
Fogg, M.J.5
Brannigan, J.A.6
Wilson, K.S.7
Wilkinson, A.J.8
-
40
-
-
84864199587
-
ZINC: A free tool to discover chemistry for biology
-
Irwin, J. J.; Sterling, T.; Mysinger, M. M.; Bolstad, E. S.; Coleman, R. G. ZINC: A free tool to discover chemistry for biology J. Chem. Inf. Model. 2012, 52, 1757-1768
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1757-1768
-
-
Irwin, J.J.1
Sterling, T.2
Mysinger, M.M.3
Bolstad, E.S.4
Coleman, R.G.5
-
41
-
-
77954036921
-
Virtual fragment docking by Glide: A validation study on 190 protein-fragment complexes
-
Sandor, M.; Kiss, R.; Keseru, G. M. Virtual fragment docking by Glide: a validation study on 190 protein-fragment complexes J. Chem. Inf. Model. 2010, 50, 1165-1172
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 1165-1172
-
-
Sandor, M.1
Kiss, R.2
Keseru, G.M.3
-
42
-
-
67650149263
-
QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors
-
Gleeson, M. P.; Gleeson, D. QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors J. Chem. Inf. Model. 2009, 49, 1437-1448
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1437-1448
-
-
Gleeson, M.P.1
Gleeson, D.2
-
43
-
-
45749095524
-
Investigation of MM-PBSA rescoring of docking poses
-
Thompson, D. C.; Humblet, C.; Joseph-McCarthy, D. Investigation of MM-PBSA rescoring of docking poses J. Chem. Inf. Model. 2008, 48, 1081-1091
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 1081-1091
-
-
Thompson, D.C.1
Humblet, C.2
Joseph-Mccarthy, D.3
-
44
-
-
67650997041
-
Virtual fragment screening: An exploration of various docking and scoring protocols for fragments using Glide
-
Kawatkar, S.; Wang, H.; Czerminski, R.; Joseph-McCarthy, D. Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide J. Comput.-Aided Mol. Des. 2009, 23, 527-539
-
(2009)
J. Comput.-Aided Mol. Des.
, vol.23
, pp. 527-539
-
-
Kawatkar, S.1
Wang, H.2
Czerminski, R.3
Joseph-Mccarthy, D.4
-
45
-
-
33746872935
-
Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring
-
Lyne, P. D.; Lamb, M. L.; Saeh, J. C. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring J. Med. Chem. 2006, 49, 4805-4808
-
(2006)
J. Med. Chem.
, vol.49
, pp. 4805-4808
-
-
Lyne, P.D.1
Lamb, M.L.2
Saeh, J.C.3
-
46
-
-
40649101151
-
Rescoring docking hit lists for model cavity sites: Predictions and experimental testing
-
Graves, A. P.; Shivakumar, D. M.; Boyce, S. E.; Jacobson, M. P.; Case, D. A.; Shoichet, B. K. Rescoring docking hit lists for model cavity sites: predictions and experimental testing J. Mol. Biol. 2008, 377, 914-934
-
(2008)
J. Mol. Biol.
, vol.377
, pp. 914-934
-
-
Graves, A.P.1
Shivakumar, D.M.2
Boyce, S.E.3
Jacobson, M.P.4
Case, D.A.5
Shoichet, B.K.6
-
47
-
-
0024953088
-
Mechanisms of cooperativity and allosteric regulation in proteins
-
Perutz, M. F. Mechanisms of cooperativity and allosteric regulation in proteins Q. Rev. Biophys. 1989, 22, 139-237
-
(1989)
Q. Rev. Biophys.
, vol.22
, pp. 139-237
-
-
Perutz, M.F.1
-
48
-
-
35448946080
-
Molecular dynamics simulations and their application to four-stranded DNA
-
Sponer, J.; Spackova, N. Molecular dynamics simulations and their application to four-stranded DNA Methods 2007, 43, 278-290
-
(2007)
Methods
, vol.43
, pp. 278-290
-
-
Sponer, J.1
Spackova, N.2
-
49
-
-
33644912316
-
Measuring diagnostic and predictive accuracy in disease management: An introduction to receiver operating characteristic (ROC) analysis
-
Linden, A. Measuring diagnostic and predictive accuracy in disease management: an introduction to receiver operating characteristic (ROC) analysis J. Eval. Clin. Pract. 2006, 12, 132-139
-
(2006)
J. Eval. Clin. Pract.
, vol.12
, pp. 132-139
-
-
Linden, A.1
-
50
-
-
17144385534
-
Virtual screening workflow development guided by the ″receiver operating characteristic″ curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4
-
Triballeau, N.; Acher, F.; Brabet, I.; Pin, J. P.; Bertrand, H. O. Virtual screening workflow development guided by the ″receiver operating characteristic″ curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4 J. Med. Chem. 2005, 48, 2534-2547
-
(2005)
J. Med. Chem.
, vol.48
, pp. 2534-2547
-
-
Triballeau, N.1
Acher, F.2
Brabet, I.3
Pin, J.P.4
Bertrand, H.O.5
-
51
-
-
41349084852
-
Bias, reporting, and sharing: Computational evaluations of docking methods
-
Jain, A. N. Bias, reporting, and sharing: computational evaluations of docking methods J. Comput.-Aided Mol. Des. 2008, 22, 201-212
-
(2008)
J. Comput.-Aided Mol. Des.
, vol.22
, pp. 201-212
-
-
Jain, A.N.1
-
52
-
-
13944263886
-
Comparison of automated docking programs as virtual screening tools
-
Cummings, M. D.; DesJarlais, R. L.; Gibbs, A. C.; Mohan, V.; Jaeger, E. P. Comparison of automated docking programs as virtual screening tools J. Med. Chem. 2005, 48, 962-976
-
(2005)
J. Med. Chem.
, vol.48
, pp. 962-976
-
-
Cummings, M.D.1
Desjarlais, R.L.2
Gibbs, A.C.3
Mohan, V.4
Jaeger, E.P.5
-
53
-
-
65249117481
-
Validation of molecular docking programs for virtual screening against dihydropteroate synthase
-
Hevener, K. E.; Zhao, W.; Ball, D. M.; Babaoglu, K.; Qi, J.; White, S. W.; Lee, R. E. Validation of molecular docking programs for virtual screening against dihydropteroate synthase J. Chem. Inf. Model. 2009, 49, 444-460
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 444-460
-
-
Hevener, K.E.1
Zhao, W.2
Ball, D.M.3
Babaoglu, K.4
Qi, J.5
White, S.W.6
Lee, R.E.7
-
54
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A critical assessment of docking programs and scoring functions J. Med. Chem. 2006, 49, 5912-5931
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.M.3
Clarke, B.4
Lalonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
55
-
-
79961241154
-
Docking performance of fragments and druglike compounds
-
Verdonk, M. L.; Giangreco, I.; Hall, R. J.; Korb, O.; Mortenson, P. N.; Murray, C. W. Docking performance of fragments and druglike compounds J. Med. Chem. 2011, 54, 5422-5431
-
(2011)
J. Med. Chem.
, vol.54
, pp. 5422-5431
-
-
Verdonk, M.L.1
Giangreco, I.2
Hall, R.J.3
Korb, O.4
Mortenson, P.N.5
Murray, C.W.6
-
56
-
-
0347949637
-
Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
-
Swanson, J. M.; Henchman, R. H.; McCammon, J. A. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy Biophys. J. 2004, 86, 67-74
-
(2004)
Biophys. J.
, vol.86
, pp. 67-74
-
-
Swanson, J.M.1
Henchman, R.H.2
McCammon, J.A.3
-
57
-
-
34547460183
-
Molecular evolution of affinity and flexibility in the immune system
-
Thorpe, I. F.; Brooks, C. L., III Molecular evolution of affinity and flexibility in the immune system Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 8821-8826
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 8821-8826
-
-
Thorpe, I.F.1
Brooks Iii, C.L.2
-
58
-
-
77949608591
-
Estimating absolute configurational entropies of macromolecules: The minimally coupled subspace approach
-
Hensen, U.; Lange, O. F.; Grubmuller, H. Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach PLoS One 2010, 5, e9179
-
(2010)
PLoS One
, vol.5
, pp. 9179
-
-
Hensen, U.1
Lange, O.F.2
Grubmuller, H.3
-
59
-
-
70249092883
-
Free energy calculations of glycosaminoglycan-protein interactions
-
Gandhi, N. S.; Mancera, R. L. Free energy calculations of glycosaminoglycan-protein interactions Glycobiology 2009, 19, 1103-1115
-
(2009)
Glycobiology
, vol.19
, pp. 1103-1115
-
-
Gandhi, N.S.1
Mancera, R.L.2
-
60
-
-
79952588669
-
Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. the accuracy of binding free energy calculations based on molecular dynamics simulations
-
Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations J. Chem. Inf. Model. 2011, 51, 69-82
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 69-82
-
-
Hou, T.1
Wang, J.2
Li, Y.3
Wang, W.4
-
61
-
-
83455235864
-
Improving MM-GB/SA scoring through the application of the variable dielectric model
-
Ravindranathan, K.; Tirado-Rives, J.; Jorgensen, W. L.; Guimaraes, C. R. Improving MM-GB/SA scoring through the application of the variable dielectric model J. Chem. Theory Comput. 2011, 7, 3859-3865
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 3859-3865
-
-
Ravindranathan, K.1
Tirado-Rives, J.2
Jorgensen, W.L.3
Guimaraes, C.R.4
-
63
-
-
84858146937
-
Hsp90 Inhibitors and Drugs from Fragment and Virtual Screening
-
Davies, T. G. Hyvönen, M. Springer: Heidelberg, New York, p online resource (xi, 225 p.). (accessed Oct 30, 2012)
-
Roughley, S.; Wright, L.; Brough, P.; Massey, A.; Hubbard, R. E. Hsp90 Inhibitors and Drugs from Fragment and Virtual Screening. In Topics in Current Chemistry; Davies, T. G.; Hyvönen, M., Eds.; Springer: Heidelberg, New York, 2012; p 61 online resource (xi, 225 p.). http://www.springer.com/ chemistry/organic+chemistry/book/978-3-642-27539-5 (accessed Oct 30, 2012).
-
(2012)
Topics in Current Chemistry
, pp. 61
-
-
Roughley, S.1
Wright, L.2
Brough, P.3
Massey, A.4
Hubbard, R.E.5
-
64
-
-
4444221565
-
UCSF Chimera - A visualization system for exploratory research and analysis
-
Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 2004, 25, 1605-1612
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
|