-
1
-
-
33645887230
-
Critical review of the role of HTS in drug discovery
-
Macarron R, (2006) Critical review of the role of HTS in drug discovery. Drug Discov Today 11: 277-279.
-
(2006)
Drug Discov Today
, vol.11
, pp. 277-279
-
-
Macarron, R.1
-
3
-
-
54849423239
-
Predicting selectivity and druggability in drug discovery
-
Cheng AC, (2008) Predicting selectivity and druggability in drug discovery. Annual Reports Comp Chem 4: 23-37.
-
(2008)
Annual Reports Comp Chem
, vol.4
, pp. 23-37
-
-
Cheng, A.C.1
-
4
-
-
33846155913
-
Structure-based maximal affinity model predicts small molecule druggability
-
Cheng AC, Coleman RG, Smyth KT, Cao Q, Soulard P, et al. (2007) Structure-based maximal affinity model predicts small molecule druggability. Nature Biotech 25: 71-75.
-
(2007)
Nature Biotech
, vol.25
, pp. 71-75
-
-
Cheng, A.C.1
Coleman, R.G.2
Smyth, K.T.3
Cao, Q.4
Soulard, P.5
-
5
-
-
33746033147
-
Filtering in drug discovery
-
Lipinski CA, (2005) Filtering in drug discovery. Annual Reports Comp Chem 1: 155-168.
-
(2005)
Annual Reports Comp Chem
, vol.1
, pp. 155-168
-
-
Lipinski, C.A.1
-
6
-
-
79960985571
-
Structure-based druggability assessment-identifying suitable targets for small molecule therapeutics
-
Fauman EB, Rai BK, Huang ES, (2011) Structure-based druggability assessment-identifying suitable targets for small molecule therapeutics. Curr Opin Chem Biol 15: 463-468.
-
(2011)
Curr Opin Chem Biol
, vol.15
, pp. 463-468
-
-
Fauman, E.B.1
Rai, B.K.2
Huang, E.S.3
-
7
-
-
78649523910
-
Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank
-
Sheridan RP, Maiorov VN, Holloway MK, Cornell WD, Gao YD, (2010) Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank. J Chem Inf Model 50: 2029-2040.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 2029-2040
-
-
Sheridan, R.P.1
Maiorov, V.N.2
Holloway, M.K.3
Cornell, W.D.4
Gao, Y.D.5
-
8
-
-
65449159794
-
Binding site detection and druggability index from first principles
-
Seco J, Luque FJ, Barril X, (2009) Binding site detection and druggability index from first principles. J Med Chem 52: 2363-2371.
-
(2009)
J Med Chem
, vol.52
, pp. 2363-2371
-
-
Seco, J.1
Luque, F.J.2
Barril, X.3
-
9
-
-
84856776282
-
Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
-
Beuming T, Che Y, Abel R, Kim B, Shanmugasundaram V, et al. (2012) Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization. Proteins 80: 871-883.
-
(2012)
Proteins
, vol.80
, pp. 871-883
-
-
Beuming, T.1
Che, Y.2
Abel, R.3
Kim, B.4
Shanmugasundaram, V.5
-
10
-
-
37249004920
-
Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
-
Wells JA, McClendon CL, (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450: 1001-1009.
-
(2007)
Nature
, vol.450
, pp. 1001-1009
-
-
Wells, J.A.1
McClendon, C.L.2
-
11
-
-
34547583152
-
Transient pockets on protein surfaces involved in protein-protein interaction
-
Eyrisch S, Helms V, (2007) Transient pockets on protein surfaces involved in protein-protein interaction. J Med Chem 50: 3457-3464.
-
(2007)
J Med Chem
, vol.50
, pp. 3457-3464
-
-
Eyrisch, S.1
Helms, V.2
-
12
-
-
84876546810
-
2P2Idb: A Structural Database Dedicated to Orthosteric Modulation of Protein-Protein Interactions
-
Basse MJ, Betzi S, Bourgeas R, Bouzidi S, Chetrit B, et al. (2013) 2P2Idb: A Structural Database Dedicated to Orthosteric Modulation of Protein-Protein Interactions. Nucleic Acid Research 41: D824-827.
-
(2013)
Nucleic Acid Research
, vol.41
-
-
Basse, M.J.1
Betzi, S.2
Bourgeas, R.3
Bouzidi, S.4
Chetrit, B.5
-
13
-
-
65249117514
-
Identifying and characterizing binding sites and assessing druggability
-
Halgren TA, (2009) Identifying and characterizing binding sites and assessing druggability. J Chem Inf Model 49: 377-389.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 377-389
-
-
Halgren, T.A.1
-
14
-
-
84863052839
-
Fragment based drug discovery: practical implementation based on 19F NMR spectroscopy
-
Jordan JB, Poppe L, Xia X, Cheng AC, Sun Y, et al. (2012) Fragment based drug discovery: practical implementation based on 19F NMR spectroscopy. J Med Chem 55: 678-687.
-
(2012)
J Med Chem
, vol.55
, pp. 678-687
-
-
Jordan, J.B.1
Poppe, L.2
Xia, X.3
Cheng, A.C.4
Sun, Y.5
-
15
-
-
84880625796
-
Structure guided design of a series of sphingosine kinase (SphK) inhibitors
-
Gustin DJ, Li Y, Brown ML, Min X, Schmitt MJ, et al. (2013) Structure guided design of a series of sphingosine kinase (SphK) inhibitors. Bioorg Med Chem Lett 23: 4608-4616.
-
(2013)
Bioorg Med Chem Lett
, vol.23
, pp. 4608-4616
-
-
Gustin, D.J.1
Li, Y.2
Brown, M.L.3
Min, X.4
Schmitt, M.J.5
-
16
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R, (2006) Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 49: 534-553.
-
(2006)
J Med Chem
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
-
17
-
-
77956308900
-
Binding-site assessment by virtual fragment screening
-
Huang N, Jacobson MP, (2010) Binding-site assessment by virtual fragment screening. PLoS One 5: e10109.
-
(2010)
PLoS One
, vol.5
-
-
Huang, N.1
Jacobson, M.P.2
-
18
-
-
80051966197
-
Structural conservation of druggable hot spots in protein-protein interfaces
-
Kozakov D, Hall DR, Chuang GY, Cencic R, Brenke R, et al. (2011) Structural conservation of druggable hot spots in protein-protein interfaces. Proc Natl Acad Sci USA 108: 13528-13533.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 13528-13533
-
-
Kozakov, D.1
Hall, D.R.2
Chuang, G.Y.3
Cencic, R.4
Brenke, R.5
-
19
-
-
84886389108
-
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots
-
Grove LE, Hall DR, Beglov D, Vajda S, Kozakov D, (2013) FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinformatics 29: 1218-1219.
-
(2013)
Bioinformatics
, vol.29
, pp. 1218-1219
-
-
Grove, L.E.1
Hall, D.R.2
Beglov, D.3
Vajda, S.4
Kozakov, D.5
-
20
-
-
84863661333
-
Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules
-
Bakan A, Nevins N, Lakdawala AS, Bahar I, (2012) Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules. J Chem Theory Comput 8: 2435-2447.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 2435-2447
-
-
Bakan, A.1
Nevins, N.2
Lakdawala, A.S.3
Bahar, I.4
-
21
-
-
33746076877
-
Effects of conformational dynamics on predicted protein druggability
-
Brown SP, Hajduk PJ, (2006) Effects of conformational dynamics on predicted protein druggability. ChemMedChem 1: 70-72.
-
(2006)
ChemMedChem
, vol.1
, pp. 70-72
-
-
Brown, S.P.1
Hajduk, P.J.2
-
22
-
-
84878181372
-
TRAPP: a tool for analysis of transient binding pockets in proteins
-
Kokh DB, Richter S, Henrich S, Czodrowski P, Rippmann F, et al. (2013) TRAPP: a tool for analysis of transient binding pockets in proteins. J Chem Inf Model 53: 1235-1252.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 1235-1252
-
-
Kokh, D.B.1
Richter, S.2
Henrich, S.3
Czodrowski, P.4
Rippmann, F.5
-
23
-
-
82255164267
-
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
-
Schmidtke P, Bidon-Chanal A, Luque FJ, Barril X, (2011) MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories. Bioinformatics 27: 3276-3285.
-
(2011)
Bioinformatics
, vol.27
, pp. 3276-3285
-
-
Schmidtke, P.1
Bidon-Chanal, A.2
Luque, F.J.3
Barril, X.4
-
24
-
-
84855955506
-
A molecular dynamics ensemble-based approach for the mapping of druggable binding sites
-
Ivetac A, McCammon JA, (2012) A molecular dynamics ensemble-based approach for the mapping of druggable binding sites. Methods Mol Biol. 819: 3-12.
-
(2012)
Methods Mol Biol
, vol.819
, pp. 3-12
-
-
Ivetac, A.1
McCammon, J.A.2
-
25
-
-
78651402672
-
Full protein flexibility is essential for proper hot-spot mapping
-
Lexa KW, Carlson HA, (2011) Full protein flexibility is essential for proper hot-spot mapping. J Am Chem Soc 133: 200-202.
-
(2011)
J Am Chem Soc
, vol.133
, pp. 200-202
-
-
Lexa, K.W.1
Carlson, H.A.2
-
26
-
-
79959275847
-
How does a drug molecule find its target binding site?
-
Shan Y, Kim ET, Eastwood MP, Dror RO, Seeliger MA, et al. (2011) How does a drug molecule find its target binding site? J Am Chem Soc 133: 9181-9183.
-
(2011)
J Am Chem Soc
, vol.133
, pp. 9181-9183
-
-
Shan, Y.1
Kim, E.T.2
Eastwood, M.P.3
Dror, R.O.4
Seeliger, M.A.5
-
27
-
-
84864464925
-
FTMAP: extended protein mapping with user-selected probe molecules
-
Ngan CH, Bohnuud T, Mottarella SE, Beglov D, Villar EA, et al. (2012) FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Res 40: W271-275.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Ngan, C.H.1
Bohnuud, T.2
Mottarella, S.E.3
Beglov, D.4
Villar, E.A.5
-
28
-
-
27744586067
-
Small molecule inhibition of TNF-alpha
-
He MM, Smith AS, Oslob JD, Flanagan WM, Braisted AC, et al. (2005) Small molecule inhibition of TNF-alpha. Science 310: 1022-1025.
-
(2005)
Science
, vol.310
, pp. 1022-1025
-
-
He, M.M.1
Smith, A.S.2
Oslob, J.D.3
Flanagan, W.M.4
Braisted, A.C.5
-
29
-
-
34548047900
-
Crystal structure of ABT-737 complexed with Bcl-xL: implications for selectivity of antagonists of the Bcl-2 family
-
Lee EF, Czabotar PE, Smith BJ, Deshayes K, Zobel K, et al. (2007) Crystal structure of ABT-737 complexed with Bcl-xL: implications for selectivity of antagonists of the Bcl-2 family. Cell Death Differ 14: 1711-1713.
-
(2007)
Cell Death Differ
, vol.14
, pp. 1711-1713
-
-
Lee, E.F.1
Czabotar, P.E.2
Smith, B.J.3
Deshayes, K.4
Zobel, K.5
-
30
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 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
-
31
-
-
84861015413
-
InterEvol database: Exploring the structure and evolution of protein complex interfaces
-
Faure G, Andreani J, Guerois R, (2012) InterEvol database: Exploring the structure and evolution of protein complex interfaces. Nucleic Acids Res 40: D847-56 (Used July 2012 release from http://biodev.cea.fr/interevol/, downloaded May 26, 2013.).
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Faure, G.1
Andreani, J.2
Guerois, R.3
-
32
-
-
33845806987
-
Structure-based identification of small molecule binding sites using a free energy model
-
Coleman RG, Salzberg AC, Cheng AC, (2006) Structure-based identification of small molecule binding sites using a free energy model. J Chem Inf Model 46: 2631-2637.
-
(2006)
J Chem Inf Model
, vol.46
, pp. 2631-2637
-
-
Coleman, R.G.1
Salzberg, A.C.2
Cheng, A.C.3
-
33
-
-
84875984520
-
Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface
-
Johnson DK, Karanicolas J, (2013) Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface. PLoS Comput Biol 9: e1002951.
-
(2013)
PLoS Comput Biol
, vol.9
-
-
Johnson, D.K.1
Karanicolas, J.2
-
34
-
-
84856370676
-
Pocketome: an encyclopedia of small-molecule binding sites in 4D
-
Kufareva I, Ilatovskiy AV, Abagyan R, (2012) Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res 40: D535-40.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Kufareva, I.1
Ilatovskiy, A.V.2
Abagyan, R.3
-
35
-
-
84871901456
-
Objective assessment of cancer genes for drug discovery
-
Patel MN, Halling-Brown MD, Tym JE, Workman P, Al-Lazikani B, (2013) Objective assessment of cancer genes for drug discovery. Nat Rev Drug Discov 12: 35-50.
-
(2013)
Nat Rev Drug Discov
, vol.12
, pp. 35-50
-
-
Patel, M.N.1
Halling-Brown, M.D.2
Tym, J.E.3
Workman, P.4
Al-Lazikani, B.5
-
36
-
-
28444469788
-
Mapping PDB chains to UniProtKB entries
-
Downloaded March 6, 2013 update
-
Martin AC (2005) Mapping PDB chains to UniProtKB entries. Bioinformatics 21: 4297-4301. Downloaded March 6, 2013 update.
-
(2005)
Bioinformatics
, vol.21
, pp. 4297-4301
-
-
Martin, A.C.1
-
37
-
-
60149086624
-
bioDBnet: the biological database network
-
Mudunuri U, Che A, Yi M, Stephens RM, (2009) bioDBnet: the biological database network. Bioinformatics 25: 555-556.
-
(2009)
Bioinformatics
, vol.25
, pp. 555-556
-
-
Mudunuri, U.1
Che, A.2
Yi, M.3
Stephens, R.M.4
|