VLS-3D consulting: integration of in silico and experimental strategies, database mining to foster actionable knowledge...

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

Project evaluations, feasibility studies involving in silico approaches or combining experimental and in silico approaches (structural bioinformatics, chemoinformatics...).

Topics include:

• Structural analysis of potential protein targets, peptides, binding pockets...hot spots, warm spots..
• Compound collection preparation and analysis
  
• Early ADME-Tox
• Virtual screening: ligand-based and structure-based, consensus approaches
  
• Machine learning, data mining, active learning
  
• Hit optimization, in silico hit2lead
  
• Analysis of intermolecular interactions
• Protein-protein & protein-peptides interactions
• Protein-mAb interactions
• Protein stabilization
• Homology modeling - Molecular modeling
  
• Fragment mapping
• Docking (macromolecular, ligands, fragments...)
• Druggable pocket
  
• Data mining
• Drug repositioning
• Analysis of variants....

 If you have questions please contact me by email

Bruno.Villoutreix "@" gmail.com

The Biopharmaceutics Drug Distribution and Classification System (BDDCS)
attempts to split compounds into four classes based on their permeability
and solubility properties. There are many applications of the BDDCS system
such as trying to predict drug-drug interactions, elimination routes,
central nervous system exposure, toxicity, and environmental impacts
of drugs to cite a few of them...About 900 annotated drugs collected from PubMed
search and via mining DrugBank, DrugCentral and chemEMBL are shown,
each class is in a different color and the markers have different shapes. The figure
was prepared with DataWarrior.

 

 

Analysis of point mutations in antithrombin
using residue interaction network, Chimera
and clustering, view in Cytoscape.
The first mutation (left) is not damaging,
the second one is likely to be as confirmed
experimentally.

 

 

Look at sequences with the python tool Logomaker

 

Compound clustering - heatmap color according to tanimoto matrix
with ChemmineR