- Procacci P (2016) Reformulating the entropic
contribution of molecular docking scoring
functions. J Comput Chem 37:1819–1827 - Gilson MK, Zhou HX (2007) Calculation of
protein-ligand binding affinities. Annu Rev
Biophys Biomol Struct 36:21–42 - Bello M, Martı ́nez-Archundia M, Correa-
Basurto J (2013) Automated docking for
novel drug discovery. Expert Opin Drug Dis-
cov 8:821–834 - Bodnarchuck MS (2016) Water, water, every-
where...It’s time to stop and think. Drug
Discov Today 21:1139–1146 - Mysinger MM, Schoichet BK (2010) Rapid
context-dependent ligand desolvation in
molecular docking. J Chem Inf Model
50:1561–1573 - Ge H, Wang Y, Li C et al (2013) Molecular
dynamics-based virtual screening: accelerating
the drug discovery process by high-
performance computing. J Chem Inf Model
53:2757–2764 - Wang L, Wu Y, Deng Y et al (2015) Accurate
and reliable prediction of relative ligand bind-
ing potency in prospective drug discovery by
way of a modern free-energy calculation proto-
col and force field. J Am Chem Soc
137:2695–2703 - Lavechia A (2015) Machine-learning
approaches in drug discovery: methods and
applications. Drug Discov Today 20:318–331 - Lemmen C, Zimmermann M, Lengauer T
(2002) Multiple molecular superpositioning
as an effective tool for virtual database screen-
ing. In: Klebe G (ed) Virtual screening: an
alternative or complement to high-throughput
screening? 1st edn. Kluwer Academic Publish-
ers, Marburg - Kristensen TG, Nielsen J, Pedersen CNS
(2013) Methods for similarity-based virtual
screening. Comput Struct Biotechnol J 5:
e201302009 - Talevi A, Bruno-Blanch LE (2016) Virtual
screening applications in the search of novel
antiepileptic drug candidates. In: Talevi A,
Rocha L (eds) Antiepileptic drug discovery.
Novel Approaches. Humana Press, New York - Schneidman-Duhovny D, Dror O, Inbar Y,
Nussinov R, Wolfson HJ (2008) Deterministic
pharmacophore detection via multiple flexible
alignment of drug-like molecules. J Comput
Biol 15:737–754 - Cottrell SJ, Gillet VJ, Taylor R, Wilton DJ
(2004) Generation of multiple pharmacophore
hypothesis using multiobjective optimization
techniques. J Comput Aided Mol Des
18:665–682
37. Pirhadi S, Shiri F, Ghasemi JB (2013) Methods
and applications of structure based pharmaco-
phores in drug discovery. Curr Top Med Chem
13:1036–1047
38. Zhang Q, Muegge I (2006) Scaffold hopping
through virtual screening using 2D and 3D
similarity descriptors: ranking, voting, and con-
sensus scoring. J Med Chem 9:1536–1548
39. Kru ̈ger DM, Evers A (2010) Comparison of
structure- and ligand-based virtual screening
protocols considering hit list complementarity
and enrichment factors. ChemMedChem
5:148–158
40. Talevi A, Gavernet L, Bruno-Blanch LE (2009)
Combined virtual screening strategies. Curr
Comput Aided Drug Des 5:23–37
41. Pouliot M, Jeanmart S (2016) Pan assay inter-
ference compounds (PAINS) and other pro-
miscuous compounds in antifungal research. J
Med Chem 59:497–503
42. Walters WP, Stahl MT, Murcko MA (1998)
Virtual screening – an overview. Drug Discov
Today 3:160–178
43. Zhu T, Cao S, Su PC, Patel R, Shah D, Chokshi
HB, Szukala R, Johnson ME, Hevener KE
(2013) Hit identification and optimization in
virtual screening: practical recommendations
based upon a critical literature analysis. J Med
Chem 56:6560–6572
44. Ripphausen P, Nisius B, Pletason L, Bajorath J
(2010) Quo vadis, virtual screening? A com-
prehensive survey of prospective applications. J
Med Chem 53:8461–8467
45. Neetoo-Isseliee Z, MacKenzie AE,
Southern C, Jerman J, McIver EG, Harries N,
Taylor DL, Milligan G (2013) High-
throughput identification and characterization
of novel, species-selective GPR35 agonists. J
Pharmacol Exp Ther 344:568–578
46. Kola I, Landis J (2004) Can the pharmaceutical
industry reduce attrition rates? Nature Rev
Drug Discov 3:711–716
47. Schuster D, Laggner C, Langer T (2005) Why
drugs fail – a study on side effects in new
chemical entities. Curr Pharm Des
11:3545–3559
48. Talevi A (2016) Computatonal approaches for
innovative antiepileptic drug discovery. Expert
Opin Drug Discov 11:1001–1016
49. Brown N, Lewis RA (2006) Exploiting QSAR
methods in lead optimization. Curr Opin Drug
Discov Devel 9:419–424
50. Wong WWL, Burkowski FJ (2009) A construc-
tive approach for discovering new drug leads:
using a kernel methodology for the inverse-
QSAR problem. J Cheminform 1:4
18 Alan Talevi