Chemistry Reference
In-Depth Information
[27] Jones G.,Willett P., Glen R.,
et al.
Development and validation of a genetic algorithm for flexible
docking.
J. Mol. Biol
. 1997,
267
, 727-748.
[28] Eldridge M.D., Murray C.W., Auton T.R.,
et al.
Empirical scoring functions. 1. The develop-
ment of a fast empirical scoring function to estimate the binding affinity of ligands in receptor
complexes.
J. Comput.-Aided Mol. Des
. 1997,
11
, 425-445.
[29] Verdonk M.L., Cole J.C., Hartshorn M.,
et al.
Improved protein-ligand docking using GOLD.
Proteins
2003,
52
, 609-623.
[30] Polgar T., Keserü G.M., Ensemble docking into flexible active sites. Critical evaluation of FlexE
against JNK-3 and -secretase.
J. Chem. Inf. Model.
2006,
46
, 1795-1805.
[31] Vertex, Patent Application WO02/088101, 2002.
[32] Hajduk P.J., Greer J., A decade of fragment-based drug design: strategic advances and lessons
learned.
Nat. Rev. Drug Discov
. 2007,
6
, 211-219.
[33] McGaughey G.B., Sheridan R.P., Bayly C.I., Culberson J.C., Kreatsoulas C., Lindsley S.,
Maiorov V., Truchon J.-F., Cornell W., Comparison of topological, shape and docking methods
in virtual screening.
J. Chem. Inf. Model
. 2007,
47
, 1504-1519.
[34] Baxter E.W.,
et al
., 2-Amino-3,4-dihydroquinazolines as inhibitors of BACE-1 (-site APP
cleaving enzyme), use of structure based design to convert a micromolar hit into a nanomolar
lead.
J. Med. Chem
. 2007,
50
, 4261-4264.
[35]
MDL Available Chemicals Directory (MDL ACD)
. MDL Information Systems, San
Leandro, CA.
[36] Halgren T.A., Merck Molecular Force Field. I. Basis, form, scope, parameterization and
performance of MMFF94.
J. Comput. Chem
. 1996,
17
, 490-519.
[37] Holloway M.K., McGaughey G.B., Coburn C.A., Stachel S.J., Jones K.G., Stanton E.L., Gregro
A.R., Lai M.-T., Crouthamel M.-C., Pietrak B.L., Munshi S.K., Evaluating scoring functions
for docking and designing -secretase inhibitors.
Bioorg. Med. Chem. Lett
. 2006,
17
, 823-827.
[38] Hong L., Koelsch G., Lin X., Wu S., Terzyan S., Ghosh A.K., Zhang X.C., Tang J., Structure
of the protease domain of memapsin 2 (
β
-secretase) complexed with inhibitor.
Science
2000,
290
, 150-153.
[39] Stachel S.J., Coburn C.A., Steele T.G., Crouthamel M.-C., Pietrak B.L., Lai M.-T., Holloway
M.K., Munshi S.K., Graham S.L., Vacca J.P., Conformationally biased P3 amide replacements
of -secretase inhibitors.
Bioorg. Med. Chem. Lett
. 2006,
16
, 641-644.
[40] Rajapakse H.A., Nantermet P.G., Selnick H.G., Munshi S., McGaughey G.B., Lindsley S.R.,
Young M.B., Lai M.-T., Espeseth A.S., Shi X.-P., Colussi D., Pietrak B., Crouthamel M.-C.,
Tugusheva K., Huang Q., Xu M., Simon A.J., Kuo L., Hazuda D.J., Graham S., Vacca J.P.,
Discovery of oxadiazoyl tertiary carbinamine inhibitors of -secretase (BACE-1).
J. Med. Chem
.
2006,
49
, 7270-7273.
[41] Kraker B, Chakravorty S.J., Mosley R., Culberson J.C., Feuston B.P., Sheridan R.P., Conway
J.F., Forbes J.K., Kearsley S.K., Virtual library tool kit: Comparison of functional group queries
with Daylight and ISIS software. Unpublished work.
[42] Mosley R.T., Culberson J.C., Kraker B., Feuston B.P., Sheridan R.P., Conway J.F., Forbes J.K.,
Chakravorty S.J., Kearsley S.K., Reagent selector: using synthon analysis to visualize reagent
properties and assist in basis set selection.
J. Chem. Inf. Model
. 2005,
45
, 1439-1446.
[43] Feuston B.P., Chakravorty S.J., Conway J.F., Culberson J.C., Forbes J.K., Kraker B., Lennon
P.A., Lindsley C., McGaughey G.B., Mosley R., Sheridan R.P., Valenciano M., Kearsley S.K.,
Web enabling technology for the design, enumeration, optimization and tracking of compound
libraries.
Curr. Top. Med. Chem
. 2005,
5
, 773-783.
[44] MDL Information Systems, San Leandro, CA, www.mdli.com.
[45] Weininger D., SMILES, a chemical language and information-system. 1. Introduction to
methodology and encoding rules.
J. Chem. Inf. Comput. Sci
. 1988,
28
, 31-36.
