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 (obviously some tools require some serious training...)

  • How ? In the section Computational Biology and Chemistry about 3500 tools (online & standalone) & databases/datasets, collected over two decades, are organized in different tables. Tools are grouped into 3 main categories: Chemoinformatics, Related tools and Bioinformatics. The same "tools" can belong to different categories...To make it easier, all new tools/datasets are added to 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. If you see missing tools, send me email. For consulting see the About Me menu bar.

Last update Dec 8, 2021

In one click




New tools

Examples of tools reported by computational groups worldwide: Dec 2021


CROssBAR (biomedical knowledge graphs)

MolADI (protein-ligand interaction analysis)

ModFlex (homology modeling)

ProfKin (kinase profiling)

DeepComplex (PPI prediction)

DLAB (antibody design)

FALCON2 (protein structure prediction)

EpiSurf (epitopes of SARS-CoV-2)

BCEPS (B cell linear epitope prediction)

iRefWeb (navigating PPI landscape)

DINC-COVID (docking into Cov2 proteins - ensemble)


MolGpka (pKa prediction via Graph-Convolutional Neural Network)

PyRMD (ligand-based virtual screening - random matrix)

Antiviral Combination DB (database)

OlfactionBase (olfactory data)

PredMS (metabolic stability)

EMuSSel (polypharmacology profiling)

RealVS (ligand-based screening)

iCYP-MFE (CYP inhibitors)

B3DB (BBB compounds for machine learning)

Bruno Villoutreix

About me


Years of experience


Databases and software packages listed on this website

~730 000

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



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. 2019-2020 I worked in a drug discovery unit, U1177, in Lille and now, in INSERM unit 1141, Robert-Debré Hospital, Paris - France.  

I study undrugged 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 located in France and abroad...The approach/project involves/includes Integrative Computational Pharmacology, Data Mining & Knowledge Discovery

I am Editor in Chief of Frontiers in Drug Discovery, a new journal launched during Summer 2021. We are working on a Covid research topic dedicated to small molecules, peptides and antibodies and their therapeutic potentials (deadline early 2022).

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




Follow me

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