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...).
- Structural analysis of protein targets
- Compound collection preparation and analysis
- Early ADME-Tox
- Virtual screening
- Machine learning
- Data mining
- Active learning
- Intermolecular interactions
- Protein-protein & protein-peptides interactions
- Protein stabilization
- Homology modeling
- Molecular modeling
- Fragment mapping
- 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 - 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