-
1
-
-
67849113794
-
The rise of fragment-based drug discovery
-
Murray CW, Rees DC (2009) The rise of fragment-based drug discovery. Nat Chem 1:187-192
-
(2009)
Nat Chem
, vol.1
, pp. 187-192
-
-
Murray, C.W.1
Rees, D.C.2
-
5
-
-
43049088827
-
Ligand binding efficiency: Trends, physical basis, and implications
-
Reynolds CH, Tounge BA, Bembenek SD (2008) Ligand binding efficiency: trends, physical basis, and implications. J Med Chem 51: 2432-2438
-
(2008)
J Med Chem
, vol.51
, pp. 2432-2438
-
-
Reynolds, C.H.1
Tounge, B.A.2
Bembenek, S.D.3
-
8
-
-
79958851565
-
Ligand effi-ciency indices (LEIs): More than a simple effi-ciency yardstick
-
Abad-Zapatero C, Blasi D (2011) Ligand effi-ciency indices (LEIs): more than a simple effi-ciency yardstick. Mol Informatics 30:122-132
-
(2011)
Mol Informatics
, vol.30
, pp. 122-132
-
-
Abad-Zapatero, C.1
Blasi, D.2
-
9
-
-
79958844315
-
Retrospective mapping of SAR data for TTR protein in chemico-biological space using ligand effi-ciency indices as a guide to drug discovery strategies
-
Blasi D, Arsequell G, Valencia G, Nieto J, Planas A, Pinto M et al (2011) Retrospective mapping of SAR data for TTR protein in chemico-biological space using ligand effi-ciency indices as a guide to drug discovery strategies. Mol Informatics 30:161-167
-
(2011)
Mol Informatics
, vol.30
, pp. 161-167
-
-
Blasi, D.1
Arsequell, G.2
Valencia, G.3
Nieto, J.4
Planas, A.5
Pinto, M.6
-
10
-
-
79851483555
-
A practical use of ligand efficiency indices out of the fragment-based approach: Ligand efficiencyguided lead identification of soluble epoxide hydrolase inhibitors
-
Tanaka D, Tsuda Y, Shiyama T, Nishimura T, Chiyo N, Tominaga Y et al (2010) A practical use of ligand efficiency indices out of the fragment-based approach: ligand efficiencyguided lead identification of soluble epoxide hydrolase inhibitors. J Med Chem 54:851-857
-
(2010)
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
-
12
-
-
34249050729
-
Identification of inhibitors of protein kinase B using fragment-based lead discovery
-
Saxty G, Woodhead SJ, Berdini V, Davies TG, Verdonk ML, Wyatt PG et al (2007) Identification of inhibitors of protein kinase B using fragment-based lead discovery. J Med Chem 50:2293-2296
-
(2007)
J Med Chem
, vol.50
, pp. 2293-2296
-
-
Saxty, G.1
Woodhead, S.J.2
Berdini, V.3
Davies, T.G.4
Verdonk, M.L.5
Wyatt, P.G.6
-
13
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford PJ (1985) A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 28:849-857
-
(1985)
J Med Chem
, vol.28
, pp. 849-857
-
-
Goodford, P.J.1
-
14
-
-
84866151593
-
MM-ISMSA: An ultrafast and accurate scoring function for protein-protein docking
-
Klett J, Nuñez-Salgado A, Dos Santos HG, Cortés-Cabrera Á, Perona A, Gil-Redondo R et al (2012) MM-ISMSA: an ultrafast and accurate scoring function for protein-protein docking. J Chem Theor Comput 8:3395-3408
-
(2012)
J Chem Theor Comput
, vol.8
, pp. 3395-3408
-
-
Klett, J.1
Nuñez-Salgado, A.2
Dos Santos, H.G.3
Cortés-Cabrera, Á.4
Perona, A.5
Gil-Redondo, R.6
-
15
-
-
0031226772
-
Empirical scoring functions: I
-
Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 11:425-445
-
(1997)
The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
16
-
-
84874111137
-
A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: Methods behind the HYDE scoring function
-
Schneider N, Lange G, Hindle S, Klein R, Rarey M (2013) A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function. J Comput Aided Mol Des 27:15-29
-
(2013)
J Comput Aided Mol Des
, vol.27
, pp. 15-29
-
-
Schneider, N.1
Lange, G.2
Hindle, S.3
Klein, R.4
Rarey, M.5
-
17
-
-
34447548576
-
Ligand efficiency indices for effective drug discovery
-
Abad-Zapatero C (2007) Ligand efficiency indices for effective drug discovery. Expert Opin Drug Discov 2:469-488
-
(2007)
Expert Opin Drug Discov
, vol.2
, pp. 469-488
-
-
Abad-Zapatero, C.1
-
18
-
-
20444451242
-
The discovery of novel protein kinase inhibitors by using fragment-based high-throughput x-ray crystallography
-
Gill A, Cleasby A, Jhoti H (2005) The discovery of novel protein kinase inhibitors by using fragment-based high-throughput x-ray crystallography. Chembiochem 6:506-512
-
(2005)
Chembiochem
, vol.6
, pp. 506-512
-
-
Gill, A.1
Cleasby, A.2
Jhoti, H.3
-
19
-
-
0024566942
-
New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure
-
Boobbyer DN, Goodford PJ, Mc Whinnie PM, Wade RC (1989) New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J Med Chem 32:1083-1094
-
(1989)
J Med Chem
, vol.32
, pp. 1083-1094
-
-
Boobbyer, D.N.1
Goodford, P.J.2
McWhinnie, P.M.3
Wade, R.C.4
-
20
-
-
84879360909
-
Ins and outs of kinase DFG motifs
-
Treiber DK, Shah NP (2013) Ins and outs of kinase DFG motifs. Chem Biol 20:745-746
-
(2013)
Chem Biol
, vol.20
, pp. 745-746
-
-
Treiber, D.K.1
Shah, N.P.2
-
21
-
-
41249091782
-
Pybel: A python wrapper for the Open Babel cheminformatics toolkit
-
O'Boyle NM, Morley C, Hutchison GR (2008) Pybel: a python wrapper for the Open Babel cheminformatics toolkit. Chem Cent J 2:5
-
(2008)
Chem Cent J
, vol.2
, pp. 5
-
-
O'Boyle, N.M.1
Morley, C.2
Hutchison, G.R.3
-
23
-
-
0028466540
-
Comparison of automatic three-dimensional model builders using 639 X-ray structures
-
Sadowski J, Gasteiger J, Klebe G (1994) Comparison of automatic three-dimensional model builders using 639 X-ray structures. J Chem Inf Comput Sci 34:1000-1008
-
(1994)
J Chem Inf Comput Sci
, vol.34
, pp. 1000-1008
-
-
Sadowski, J.1
Gasteiger, J.2
Klebe, G.3
-
25
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring
-
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-1749
-
(2004)
1. Method and assessment of docking accuracy. J Med Chem
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
-
26
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren GL, Andrews CW, Capelli A-M, Clarke B, La Londe J, Lambert MH et al (2006) A critical assessment of docking programs and scoring functions. J Med Chem 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
La Londe, J.5
Lambert, M.H.6
-
27
-
-
48149114539
-
Towards an integrated description of hydrogen bonding and dehydration: Decreasing false positives in virtual screening with the HYDE scoring function
-
Reulecke I, Lange G, Albrecht J, Klein R, Rarey M (2008) Towards an integrated description of hydrogen bonding and dehydration: decreasing false positives in virtual screening with the HYDE scoring function. Chem Med Chem 3:885-897
-
(2008)
Chem Med Chem
, vol.3
, pp. 885-897
-
-
Reulecke, I.1
Lange, G.2
Albrecht, J.3
Klein, R.4
Rarey, M.5
-
28
-
-
34547559704
-
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G et al (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35:W522-W525
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 522-525
-
-
Dolinsky, T.J.1
Czodrowski, P.2
Li, H.3
Nielsen, J.E.4
Jensen, J.H.5
Klebe, G.6
-
29
-
-
0345269288
-
Virtual screening for submicromolar leads of t RNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis
-
Brenk R, Naerum L, Gradler U, Gerber HD, Garcia GA, Reuter K et al (2003) Virtual screening for submicromolar leads of t RNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis. J Med Chem 46:1133-1143
-
(2003)
J Med Chem
, vol.46
, pp. 1133-1143
-
-
Brenk, R.1
Naerum, L.2
Gradler, U.3
Gerber, H.D.4
Garcia, G.A.5
Reuter, K.6
-
30
-
-
67650097331
-
Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy
-
Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y et al (2009) Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J Chem Inf Model 49:1455-1474
-
(2009)
J Chem Inf Model
, vol.49
, pp. 1455-1474
-
-
Cross, J.B.1
Thompson, D.C.2
Rai, B.K.3
Baber, J.C.4
Fan, K.Y.5
Hu, Y.6
-
31
-
-
80053512597
-
Open babel: An open chemical toolbox
-
O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open babel: an open chemical toolbox. J Cheminform 3:33
-
(2011)
J Cheminform
, vol.3
, pp. 33
-
-
O'Boyle, N.M.1
Banck, M.2
James, C.A.3
Morley, C.4
Vandermeersch, T.5
Hutchison, G.R.6
-
32
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 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
-
33
-
-
0017884417
-
The hydrophobic effect and the organization of living matter
-
Tanford C (1978) The hydrophobic effect and the organization of living matter. Science 200:1012-1018
-
(1978)
Science
, vol.200
, pp. 1012-1018
-
-
Tanford, C.1
-
34
-
-
0030979125
-
Automatic identification and representation of protein binding sites for molecular docking
-
Ruppert J, Welch W, Jain AN (1997) Automatic identification and representation of protein binding sites for molecular docking. Proc Natl Acad Sci U S A 6:524-533
-
(1997)
Proc Natl Acad Sci U S A
, vol.6
, pp. 524-533
-
-
Ruppert, J.1
Welch, W.2
Jain, A.N.3
-
35
-
-
0000238336
-
A simplex method for function minimization
-
Nelder JA, Mead R (1965) A simplex method for function minimization. Comput J 7:308-313
-
(1965)
Comput J
, vol.7
, pp. 308-313
-
-
Nelder, J.A.1
Mead, R.2
|