vls3d.com: directory of tools & databases collected over 20 years

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

  • If you have no time to read this short introduction, you can find most URLs on one single page here: SHORTLIST page
  • Keywords: in silico drug design, hit2lead, virtual screening, structural bioinformatics, computational pharmacology, ADME-Tox, PPI, network, mutations/variations, chemical space, binding pockets, data mining, machine learning/AI...

  • Philosophy: Find the tools/datasets you need for your project

  • How ? About 3900 tools (online & standalone) & databases/datasets have been collected over two decades. Some services are now closed. All the tools/datasets are posted in the shortlist page.
  • History: ~500 links were first published by Villoutreix et al. in Curr Protein Pept Sci. 2007, 8:381-411 & Curr Protein Pept Sci. 2002, 3:341-364. When this site was launched, the focus was on Virtual Ligand Screening and structural (3D) bioinformatics (VLS3D). Since then, other 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 or Singh, Chaput and Villoutreix, Briefings in Bioinformatics.
I'll do my best to remove dead content twice a year. For consulting see the About Me menu bar.

Last update June 8, 2023

New tools

Examples of tools reported by computational groups worldwide: May-June 2023


GraphBepi (antibody design)

epitope1D (antibody design)

DeepAlloDriver (cancer driver mutations)

PASSer (allosteric pockets)

ACFIS 2.0 (fragment-based drug design)

PROST (protein homolog detection)

PEP-FOLD4 (peptide simulation)

AREA-AFFINITY (antibody-antigen affinity)

ARMADiLLO (antibody mutation probabilities)


VSTH (structure-based virtual screening)

Caverweb (screening of the FDA collection)

CovBinderInPDB (covalent binders - PDB)

HCovDock (covalent docking)

Dockey (virtual screening)

DEEPCYPs (CYP prediction)

Bruno Villoutreix

About me


Years of experience


Databases and software packages listed on this website

~800 000

Visitors since the site was launched in 2006


Articles & Reviews


Book chapters


H-Index Google scholar


Chemical "probes" identified

1 + 3

1 anti-metastatic molecule designed in silico in phase II & 3 repurposed drugs tested in animal models

14 + 5

14 Patents & 5 Software packages

I have been working at the interface between molecular medicine (mainly cancer, the complement system and blood coagulation), structural bioinformatics and chemoinformatics for over 20 years in different countries (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 was head of the research unit U973 in Paris between 2009 and 2018. I am presently working in INSERM U1141, Robert-Debré Hospital, Paris - France.  

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

I am Editor in Chief of Frontiers in Drug Discovery, a new journal launched during Summer 2021.

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 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



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