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, aa variations, chemical space, QSAR, binding pockets & hot-spots, data mining, machine learning, big data...

  • Philosophy: Find the tools you need for your project

  • How ? In the section Computational Biology and Chemistry about 3300 tools (online & standalone) & databases/datasets, collected over a decade, are organized in different tables. These tools 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. To make it easier, I tend to add tools directly in the shortlist page such as to have all at once

  • History: ~500 links were first published by Villoutreix et al. in Curr Protein Pept Sci. 2007, 8:381-411 (I started to collect them for myself in 2002, Structural Bioinformatics: Methods, Concepts and Applications to Blood Coagulation Proteins, Current Protein and Peptide Science, 2002, 3, 341-364). 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 Dec 8  2018

In one click




New tools

Examples of tools reported by computational groups worldwide Nov / Dec 2018


MTiOpenScreen (with purchasable drug repositioning option)

PYWINDOW (detect pores)

SEBOMD (simulation)



CH/PMUNK (virtual synthesizable small-molecule collections)

Mordred (molecular descriptors)



Bruno Villoutreix

About me


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 phase II 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



Since 2003, I have been a consultant for biotechnology and pharmaceutical companies as well as for academic research groups and institutes...

Some concepts & tools

In the post-genomic era, informatics technologies play a major role in medical research and pharmaceutical sciences and have become increasingly important in data management, lead-compound identification and in enhancing our understanding of the health and disease states (bioinformatics, chemoinformatics, data mining, dataviz, network...)...

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