vls3d.com: directory of tools & databases collected over 10 years

Computational Approaches and "Free" Resources to Assist Drug Discovery, Chemical Biology & Precision Medicine

  • IF you have no time to read please go to the SHORTLIST page

  • Keywords: in silico drug design, virtual screening, bioinformatics, molecular interactions, ADME-Tox, docking, amino-acid variations, compound collections, chemical space, QSAR, binding pockets & hot-spots, data mining, big data...

  • Philosophy: Find the tools you need for your project

  • How ? In the section Computational Biology and Chemistry about 2900 tools (online & standalone) & databases/datasets, organized in different tables, collected over a decade that assist drug discovery, chemical biology & research in the field of pathophysiology & precision medicine. Tools are grouped into 3 main categories: Chemoinformatics, Related tools and Bioinformatics. The same software/database can be in different tables.

  • History: ~400 "free" tools and databases were first published by Villoutreix et al. in Curr Protein Pept Sci. 2007, 8:381-411. When this site was launched in 2006, the focus was essentially on Virtual Ligand Screening and structural (3D) bioinformatics, thus the name VLS3D. Since then, some related topics have been added.

Nota Bene: If this site is helpful for your work, please cite: Villoutreix et al. Drug Discovery Today 2013, 18:1081-9
I'll do my best to remove dead content twice a year. Bruno Villoutreix

Last update Sep.   24   2017

In one click




New tools

Examples of tools reported by computational groups around the globe in August - September 2017


ToxDock (can be used for peptide docking)

Micelle Maker

STOPGAP (Systematic Target OPportunity assessment by Genetic Association Predictions)


FAF-Drugs4 (ADMET prediction, FAF-QED Bioinformatics)

AnchorQuery (update, structure-based design of PPI inhibitors)

DTINet (drug–target interactions from heterogeneous network)

Bruno Villoutreix

About me

Bruno Villoutreix
College de France
Video Inserm


Years experience in the field of in silico molecular medicine


Databases and software packages listed on this website


Visitors since the site was launched in 2006


Articles and reviews


Book chapters


H-Index Google scholar


Chemical "probes" identified


anti-metastatic molecule designed in silico now in clinical trial


Patents, mainly in the field of cancer

I have been working at the interface between molecular medicine (mainly cancer, the complement system and blood coagulation), and structural bioinformatics and chemoinformatics for over 20 years in different countries (mainly USA, Finland, Sweden, France), in the private and academic sectors.

I am research director at the Inserm Institute (the French National Institute of Health and Medical Research is a public scientific and technological institute which operates under the joint authority of the French Ministry of Health and French Ministry of Research) and head of the research unit U973.

I study many undrugged targets and mechanisms such as those involving protein-protein interactions and transient protein-membrane interactions using different types of known and novel in silico approaches, in collaboration with experimental teams located in France and abroad...

In silico drug design



I teach some master and PhD courses in the field of drug design, blood coagulation, structure-based virtual screening, ADME-tox predictions, protein modeling...

Some concepts & tools

There are many in silico tools that can be used: ADMET predictions, searching for binding pockets, investigate protein-protein interaction networks, drug repositioning, protein modeling, grafting sugar onto a protein structure, peptide docking, systems pharmacology, adverse drug reactions, annotated compound collections, virtual screening, analysis of point mutations observed in patients, protein docking...

Some Unix tips to manipulate biology and chemistry files

The idea is to have very short scripts or one line codes, very simple ones to perform some simple tasks on chemistry and protein (or other) files

Cover pages

Some illustrated examples of my work




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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira