DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit

Dimitrios Vlachakis; Paraskevas Fakourelis; Vasileios Megalooikonomou; Christos Makris; Sophia Kossida

doi:10.7717/peerj.725

DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit

PeerJ. 2015 Jan 13:3:e725. doi: 10.7717/peerj.725. eCollection 2015.

Authors

Dimitrios Vlachakis^#^{1

2}, Paraskevas Fakourelis^#^{1

2}, Vasileios Megalooikonomou², Christos Makris², Sophia Kossida^{1

3}

Affiliations

¹ Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece.
² Computer Engineering and Informatics Department, University of Patras, Patras, Greece.
³ IMGT, Laboratoire d'ImmunoGénétique Moléculaire, Institut de Génétique Humaine, Montpellier, France.

^# Contributed equally.

Abstract

During the past few years, pharmacophore modeling has become one of the key components in computer-aided drug design and in modern drug discovery. DrugOn is a fully interactive pipeline designed to exploit the advantages of modern programming and overcome the command line barrier with two friendly environments for the user (either novice or experienced in the field of Computer Aided Drug Design) to perform pharmacophore modeling through an efficient combination of the PharmACOphore, Gromacs, Ligbuilder and PDB2PQR suites. Our platform features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process. For the pharmacophore modeling we are focusing on either the characteristics of the receptor or the full molecular system, including a set of selected ligands. DrugOn can be freely downloaded from our dedicated server system at www.bioacademy.gr/bioinformatics/drugon/.

Keywords: 3D structure; Drug design; Modelling; Pharmacophore.

Grants and funding

This work was partially supported by (1) The BIOEXPLORE research project (BIOEXPLORE research project falls under the Operational Program “Education and Lifelong Learning” and it is co-financed by the European Social Fund (ESF) and National Resources), and by (2) the European Union (European Social Fund—ESF) and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF)—Research Funding Program: Thales. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.