Structure-based three-dimensional pharmacophores as an alternative to traditional methodologies

Figures & data

Figure 1 Graphic representation of results obtained by searching PubMed using a keyword structure-based pharmacophore.

Figure 2 Classification of pharmacophore development methods.

Table 1 Overview of tools available for structure-based pharmacophore modeling

Name of tool	Modes	Virtual screening capability	Studies reported in PubMed (n)
LigandScout^a	Ligand-target complex-based	Yes	<20
DS Catalyst^b	Ligand-target complex/target structure-based	Yes	>20
e-Pharmacophore^c	Ligand-target complex-based	Yes	<15
Shape4^d	Target structure-based	No	2
Pocket v.2^e	Ligand-target complex-based	No	2
Snooker^f	Target structure-based	No	1

Notes:

a Inte:Ligand GmbH, Vienna, Austria;

b Accelrys, San Diego, CA, USA;

c Schrödinger, LLC, New York, NY, USA;

d Department of Pharmaceutical Sciences, Biomanufacturing Research Institute Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, USA;

e Institute of Physical Chemistry, Peking University, People’s Republic of China; and

f Computational Drug Discovery Group, CMBI, Radboud University Nijmegen, the Netherlands.

Abbreviations: DS, Discovery Studio; e-Pharmacophore, energy-optimized Pharmacophore; v, version.