Computational Biology & Bioinformatics
Structural and computational analysis — docking, MD simulation, and drug-target interaction studies.
Overview
This is structural and computational biology at research depth: molecular docking, molecular dynamics simulation, mutation analysis and drug-target interaction studies, built on direct experience running these pipelines for HIV-1 protease resistance and related structural biology work.
Engagements range from a single docking study to a full simulation campaign with statistical analysis and figure preparation for publication.
How it works
System definition
Defining the target, ligands, and biological question the analysis needs to answer.
Pipeline setup
Configuring the computational pipeline — commonly AutoDock Vina and GROMACS.
Simulation & analysis
Running simulations and analysing trajectories, binding energies, or structural changes.
Interpretation & reporting
A written interpretation of results, with figures ready for a manuscript or report.
Benefits
Publication-ready structural analysis without an in-house computational biologist
Access to GROMACS and AutoDock Vina expertise
Statistically sound simulation design from the outset
Clear, plain-language interpretation of complex structural data
Frequently asked questions
Primarily AutoDock Vina for docking and GROMACS for molecular dynamics, alongside PyMOL and ChimeraX for structural visualisation.
Yes — reviewing and reinterpreting existing simulation or docking data is a common starting point.
Not necessarily; work can be run on independently maintained infrastructure, or on yours if preferred.
Yes, including figure preparation and methods-section-ready documentation.