Computational Chemistry

Unleashing the Power of Simulation.

Challenging Ideas™

A close synergistic integration with medicinal chemistry, biology (suggest mutants for POC) and IP groups led us to predict and Challenge Ideas™.

Our target is to bring a very grounded and pragmatic approach with a strong emphasis on synthetic feasibility as data needs to be actionable.

Our computational chemistry scientists work very closely with our medicinal chemistry team for a uniquely efficient evaluation and alignment of project fundamentals and align thinking.

  • Optimize existing structural model
  • Validate docking protocol
  • Support medicinal chemistry to establish SAR


Data Management
  • Databases clean-up and preparation
  • Cross format data (e.g. from TXT to SDF)
  • 2D-to-3D chemical structures
  • Data clustering and filtering
Property Calculations
  • Physicochemical and thermochemical descriptors calculation (i.e. LogP, TPSA, molecular weight, acidity/basicity, …)
  • CNS MPO and BBB scores calculations
Quantum Mechanics
  • Ligand conformation analysis and energy evaluation
  • Orbital calculation (HOMO, LUMO, reactivity indices, charge)
  • Interaction analysis
  • Organic reaction and transition state analysis
  • Potential energy surface (reaction mechanism) exploration

Special Platform

  • Protacs development through end ligands
  • Linker design and optimization
Illimited Computational Power
  • Internal servers for day-to-day computing
  • On demand external server with state-of-the-art security for:
    • Docking
    • Virtual screening
    • Molecular dynamics

Protein/Ligand & Protein/Protein Interactions

Building a Docking Model
  • Assessment of available structures (crystallographic data and AlphaFold model)
  • Generation of homology models
  • Docking protocol creation and validation
Virtual Screening
  • Selection of suitable candidates for virtual screening from large library of commercial compounds
  • Generation of combinatorial libraries based on current synthetic approaches
  • Selection based on desired parameters
Structure Activity Relationship (SAR)
  • Quantitative model elaboration
  • SAR model elaboration
New Chemical Matter
  • IP landscape analysis
  • Scaffold modification/replacement
  • De Novo scaffold design
Protein/Protein Model
  • Protein surface (contacts, hydrophilic-hydrophobic hot-spots, electrostatic, and surface area and pocket volume) analysis
  • Antibody interaction analysis
  • Protein/protein docking

Protein Motions in Drug Discovery

Molecular Dynamics
  • Simulation of free and bound protein
  • Identification of principal motions
  • Analysis of the protein function and drug molecule’s mechanism
  • Binding site identification and analysis
  • Ligand binding refinement
  • Clustering (RMSD), interaction (Occupancy), motion (RMSF, PCA) and correlation analysis