SERVICES
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
Cheminformatics
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
- 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