DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit

, , ,
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
DOI
10.7287/peerj.preprints.668v1
Published
Accepted
Subject Areas
Bioinformatics, Computational Biology, Pharmacology, Computational Science
Keywords
modelling, pharmacophore, drug design, 3D structure
Copyright
© 2014 Vlachakis et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Vlachakis D, Fakourelis P, Makris C, Kossida S. 2014. DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit. PeerJ PrePrints 2:e668v1

Abstract

During the past years pharmacophore modeling has become one of the key components in computer-aided drug design and generally 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/

Author Comment

This is a revised version of a manuscript submitted to PeerJ.

Supplemental Information

Figure S1

A flowchart of the DrugOn pipeline.

DOI: 10.7287/peerj.preprints.668v1/supp-1

Figure S2

The 5-HT1B-BRIL use case benchmark of DrugOn. Here is the 3D alignment of the qualifying molecules for the given receptor. A) The MOE result, B) The Schrödinger result and C) the DrugOn result.

DOI: 10.7287/peerj.preprints.668v1/supp-2

Figure S3

The PARN use case benchmark of DrugOn. Top: The 3D alignment of the qualifying molecules for the catalytic site of PARN. On the left is the MOE output while on the right is the DrugOn result. Bottom: The final 3D pharmacophore model for PARN. The MOE output is on the Left while the DrugOn 3D pharmacophore is on the right. The results are almost identical and have been confirmed in vitro by enzymatic biological assays.

DOI: 10.7287/peerj.preprints.668v1/supp-3

Results for the validation requested by the reviewers

This is the raw dataset of the validation requested by the reviewers

DOI: 10.7287/peerj.preprints.668v1/supp-6