Molecular simulation for PhD researchers and research groups

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

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

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

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

Build topologies, solvate and neutralise, minimise, equilibrate in NVT then NPT, run production, then correct periodic boundaries before analysis.

MM/PBSA estimates binding energy from MD snapshots. It ranks similar ligands reasonably well but is not an exact measure of affinity.

Prepare the target and library, filter by properties, validate the docking setup, dock, then rank, cluster and inspect before choosing compounds to test.