About

Who runs the site

InSilicoBench is written, tested and maintained by Yassir Boulaamane, a postdoctoral researcher in computational drug discovery at the Universitat Autònoma de Barcelona. It covers the computational side of early-stage drug discovery:

• Structure-based methods: molecular docking, molecular dynamics with GROMACS, and binding free energy estimates such as MM-PBSA/MM-GBSA.
• Ligand-based methods and data: QSAR, bioactivity data curation and cheminformatics.

Every article and tool is written and checked by him. His background, research and public profiles (ORCID, Google Scholar) are on the author page.

Postdoctoral researcher, computational drug discovery Yassir Boulaamane Postdoctoral researcher at the Universitat Autònoma de Barcelona (InSiliChem), with a PhD in computational drug discovery. Works on molecular docking, molecular dynamics, free energy calculations and machine-learning QSAR. Molecular docking · Molecular dynamics (GROMACS) · MM-PBSA / MM-GBSA · QSAR and machine learning for molecular properties · Drug metabolism (cytochrome P450)

Why this site exists

Many docking, MD and free energy tutorials online were written for software versions that are now years old. Commands break, flags get renamed, defaults change, and pipelines quietly give different answers. This site aims to be the reference I wish I had had:

• Tutorials pinned to specific versions, showing the expected output at each step.
• Troubleshooting pages built from errors people actually hit.
• Small browser tools for the calculations and sanity checks that come up every week, such as checking an .mdp file, converting IC50 to Ki, or defining a docking box.

How content is produced

Commands are run on real Linux workstations against the versions listed at the top of each tutorial. Where a tutorial shows program output, it comes from those runs. The tools' logic is covered by unit tests, and the GROMACS templates are checked with gmx grompp. Read the full editorial & AI-use policy.

Elsewhere

• Services by Yassir Boulaamane for docking / MD projects: services
• New articles by email: newsletter or the RSS feed
• Contact: contact page