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 Jan 24, 2021
Bruno Villoutreix
About me
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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
Introduction
