- Fechner U, Schneider G (2007) Flux (2):
comparison of molecular mutation and cross-
over operators for ligand-based de novo
design. J Chem Inf Model 47:656–667
- Dey F, Cafl isch A (2008) Fragment-basedde
novoligand design by multi objective evolu-
tionary optimization. J Chem Inf Model
48:679–690
- Hartenfeller M, Proschak E, Schu ̈ller A,
Schneider G (2008) Concept of combinato-
rialde novodesign of drug-like molecules by
particle swarm optimization. Chem Biol Drug
Des 72:16–26
- Hecht D, Fogel GB (2009) Novelin silico
approach to drug discovery via computational
intelligence. J Chem Inf Model
49:1105–1121
- Moriaud F, Doppelt-Azeroual O, Martin L,
Oguievetskaia K, Koch K, Vorotyntsev A,
Adcock SA, Delfaud F (2009) Computational
fragment-based approach at PDB scale by
protein local similarity. J Chem Inf Model
49:280–294
- Nicolaou CA, Apostolakis J, Pattichis CS
(2009)De novodrug design using multiobjec-
tive evolutionary graphs. J Chem Inf Model
49:295–307
- Durrant JD, Amaro RE, McCammon JA
(2009) AutoGrow: a novel algorithm for pro-
tein inhibitor design. Chem Biol Drug Des
73:168–178
- TY T, Chang KW, Chen CY (2011) iScreen:
world’s first cloud-computing web server for
virtual screening andde novo drug design
based on TCM database@Taiwan. J Comput
Aided Mol Des 25:525–531
- Pettersen EF, Goddard TD, Huang CC,
Couch GS, Greenblatt DM, Meng EC, Ferrin
TE (2004) UCSF chimera—a visualization
system for exploratory research and analysis.
J Comput Chem 25:1605–1612
- Eswar N, Webb B, Marti-Renom MA, Mad-
husudhan MS, Eramian D, Shen MY,
Pieper U, Sali A (2007) Comparative protein
structure modeling using MODELLER. Curr
Protoc Protein Sci 50(2.9):2.9.1–2.9.31
- Wang R, Liu L, Lai L, Tang Y (1998)
SCORE: a new empirical method for estimat-
ing the binding affinity of a protein-ligand
complex. Mol Model Ann 4:379–394
- Lagorce D, Sperandio O, Galons H, Miteva
MA, Villoutreix BO (2008) FAF-Drugs2: free
ADME/tox filtering tool to assist drug dis-
covery and chemical biology projects. BMC
Bioinformatics 9:396
- Reutlinger M, Koch CP, Reker D,
Todoroff N, Schneider P, Rodrigues T,
Schneider G (2013) Chemically advanced
template search (CATS) for scaffold-hopping
and prospective target prediction for‘orphan’-
molecules. Mol Inform 32:133–138
- Trott O, Olson AJ (2010) AutoDock Vina:
improving the speed and accuracy of docking
with a new scoring function, efficient optimi-
zation, and multithreading. J Comput Chem
31:455–461
- Hess B, Kutzner C, Van Der Spoel D, Lindahl
E (2008) GROMACS 4: algorithms for
highly efficient, load-balanced, and scalable
molecular simulation. J Chem Theory Com-
put 4:435–447
- Schro ̈dinger Release 2017–1: SiteMap,
Schro ̈dinger, LLC, New York, NY, 2017
- Selvaraj C, Priya RB, Lee JK, Singh SK (2015)
Mechanistic insights of SrtA-LPXTG blockers
targeting the transpeptidase mechanism in
Streptococcus mutans. RSC Adv
5:100498–100510
- Yang J, Roy A, Zhang Y (2013) Protein-
ligand binding site recognition using comple-
mentary binding-specific substructure com-
parison and sequence profile alignment.
Bioinformatics 29:2588–2595
- Singh S, Prabhu SV, Suryanarayanan V,
Bhardwaj R, Singh SK, Dubey VK (2016)
Molecular docking and structure based virtual
screening studies of potential drug target,
CAAX prenyl proteases, of Leishmania dono-
vani. J Biomol Struct Dyn 34(11):2367–2386
- Sastry GM, Adzhigirey M, Day T,
Annabhimoju R, Sherman W (2013) Protein
and ligand preparation: Parameters, proto-
cols, and influence on virtual screening
enrichments. J Comput Aid Mol Des
27:221–234
- Bhattacharya D, Nowotny J, Cao R, Cheng J
(2016) 3Drefine: an interactive web server for
efficient protein structure refinement. Nucleic
Acids Res 44:W406–W409
- Reddy KK, Singh SK (2015) Insight into the
binding mode between N-methyl Pyrimi-
dones and prototype foamy virus integrase-
DNA complex by QM-polarized ligand dock-
ing and molecular dynamics simulations. Curr
Top Med Chem 15:43–49
- Aarthy M, Panwar U, Selvaraj C, Singh SK
(2017) Advantages of structure-based drug
design approaches in neurological disorders.
Curr Neuropharmacol 15(8):1136–1155.
https://doi.org/10.2174/
1570159X15666170102145257
- Schro ̈dinger Release 2017–1: QikProp,
Schro ̈dinger, LLC, New York, NY, 2017
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