Computational drug discovery services

Online protein–ligand molecular docking: structure and ligand preparation, binding-site definition, pose ranking, interaction analysis and a full report.

GROMACS molecular dynamics simulation of protein–ligand complexes with equilibration, production run and full trajectory analysis (RMSD, RMSF, Rg, SASA, H-bonds, PCA, FEL).

Ligand preparation for docking and virtual screening: standardisation, protonation and tautomer states, 3D generation, energy minimisation and format conversion.

Protein homology modelling from sequence: template search, alignment, 3D model building and structure validation (Ramachandran, clash and quality scores).

In silico ADME and drug-likeness prediction: Lipinski and Veber rules, physicochemical descriptors, solubility, permeability and toxicity alerts for compound prioritisation.

2D QSAR modelling from your activity data: descriptor calculation, feature selection, model building, internal and external validation, applicability domain and predictions.

Structure-based virtual screening of compound libraries: library preparation, high-throughput docking, filtering and a ranked, traceable hit list.

Analysis of your existing molecular dynamics trajectories: RMSD, RMSF, radius of gyration, SASA, hydrogen bonds, contacts, PCA, clustering and free-energy landscapes.

MM/PBSA and MM/GBSA binding free-energy estimates from molecular dynamics trajectories, with frame selection, energy decomposition and uncertainty reported.

Preparing and screening selected ZINC20 compound subsets: subset selection, property filtering, ligand preparation, docking and ranked hit lists, subject to data availability and scope.