VLS3D Consulting

VLS-3D consulting: integration of AI-assisted in silico drug design methods, 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...

For instance: project evaluations, feasibility studies involving in silico approaches or combining experimental and in silico approaches (structural bioinformatics, chemoinformatics...).

Topics include:

  • Structural analysis of protein targets
  • Compound collection preparation and analysis
  • Early ADME-Tox
  • Virtual screening
  • Machine learning
  • Data mining
  • Active learning
  • Hit2lead
  • Intermolecular interactions
  • Protein-protein & protein-peptides interactions
  • Protein stabilization
  • Homology modeling
  • Molecular modeling
  • Fragment mapping
  • Docking
  • Druggable pocket prediction<
  • Drug repositioning
  • Analysis of variants in 3D...

If you have questions please contact me by email

Analysis of about 900 approved drugs

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 ChEMBL 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 identified in patients

Analysis of point mutations in antithrombin using residue interaction network and clustering, view in Cytoscape

Protein sequence analysis

Look at sequences with the python tool Logomaker

Compound clustering

Compound clustering - heatmap color according to tanimoto matrix with ChemmineR

AI-assisted drug design workflows:
INPUT target(s) or proposed by the method

OUTPUT: short list of molecules to assess in vitro

I combine selected machine learning algorithms, chemoinformatics and structural bioinformatics open packages, various chemistry toolkits with code from my team and I collect and curate data from various sources to develop drug design workflows