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, docking, mutations/variations, chemical space, binding pockets, data mining, machine learning/AI...

  • Philosophy: Find the tools/datasets you need for your project (warning: obviously some tools require some serious training...)

  • How ? In the section Computational Biology and Chemistry about 3300 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. Of course, the same "tools" can belong to different categories...To make it easier, I now tend to add all new tools/datasets directly in the shortlist page. For instance, some "tools" are dedicated to more fundamental research while others play a direct role in the initial steps of the drug discovery process. As such and as example, among all the links, about 300 involve online servers that can be used for drug discovery, from target/disease pathway validation, virtual screening, ADME-Tox to small molecule multi-parameter optimizations. Other links in this area will involve standalone applications...
  • 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. 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 Oct 15, 2020

In one click




New tools

Examples of tools reported by computational groups worldwide: Oct 2020


CoV-Seq (SARS-CoV-2 Genome Analysis)

PRosettaC (PROTAC modeling)

DockCoV2 (docking drugs in viral proteins)

Coronavirus3D (mutations, COVID-19 genomic divergence)


Virus-CKB (bioinfo and chemoinfo for Covid-19)

Virtual Rat (ADME-Tox)

GLORYx (prediction of metabolites)

Scopy (prepare compound collection)

SMARTS.plus (language to explore chemical compounds)

Bruno Villoutreix

About me


Years of experience


Databases and software packages listed on this website

~650 000

Visitors since the site was launched in 2006


Articles & Reviews


Book chapters


H-Index Google scholar


Chemical "probes" identified


anti-metastatic molecule designed in silico now in phase II clinical trial



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

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