Molecular surface of an enzyme, glowing red and blue under a single light, reflected on dark water

CompBioChem Tutorials

Step-by-step tutorials, scripts and models for enzyme simulations, from classical molecular dynamics to QM/MM reaction mechanisms.

Alexandre V. Pinto, PhD in Chemistry

High Performance Computing in Molecular Modelling Research Group, LAQV-REQUIMTE

Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto

Latest addition, October 2026 Preparing a QM/MM system Build a QM/MM model of an enzyme-ligand complex, from the PDB structure to a validated set of CP2K inputs.

Showing all 9 entries

  • Graphene oxide sheet in water with a molecule adsorbed on its surface

    Models and data

    Graphene oxide structures

    GAFF2-AIM graphene oxide sheet models in GROMACS format, from the J. Phys. Chem. B 2022 study on biomolecule adsorption.

    Jul 2022
  • Protein helices around a bound substrate shown as spheres

    QM/MM

    Static QM/MM

    Locate reactant, transition state and product geometries with the CI-NEB and dimer methods.

    Part 2 of Enzyme QM/MM with CP2K

    Mar 2023
  • Enzyme in rainbow cartoon with the ligand highlighted in magenta

    QM/MM

    Dynamic QM/MM

    Run QM/MM molecular dynamics along the reaction coordinate to obtain the free energy profile.

    Part 3 of Enzyme QM/MM with CP2K

  • Protein surface with acidic and basic residues coloured red and blue

    QM/MM

    Per-residue contributions to the barrier

    Delete residues one at a time from the reactant and transition state to measure how each one changes the activation energy.

    Part 4 of Enzyme QM/MM with CP2K

    Jun 2024
  • Protein with charged residues and an arrow showing the macrodipole vector

    QM/MM

    Transition state macrodipole

    Calculate the dipole moment of the enzyme and how it is oriented relative to the transition state.

    Part 5 of Enzyme QM/MM with CP2K

  • Overlaid backbone traces of many trajectory frames in red

    Molecular dynamics

    3D clustering of PCA vectors

    Cluster an MD trajectory on its first three principal components with DBSCAN and Gaussian mixture models, then extract the most representative frames.

    Mar 2025
  • Torsion energy profile of 1,3-propanediol from -180 to 180 degrees

    Force fields

    Parameterizing a dihedral angle

    Refit GAFF2 dihedral parameters against a quantum mechanical torsion scan.

    Nov 2025
  • Three phone screens of the CompChemKit app

    SoftwareNew

    CompChemKit

    An offline Android app for computational chemistry, with a lab notebook, literature hub, HPC workbench, structure studio and paper kit.

    Sep 2026
  • Enzyme active site with the QM region shown as ball-and-stick inside the protein ribbons

    QM/MMNew

    Preparing a QM/MM system

    Build a QM/MM model of an enzyme-ligand complex, from the PDB structure to a validated set of CP2K inputs.

    Part 1 of Enzyme QM/MM with CP2K

    Oct 2026

About

Protein cartoon in orange, pink and purple resting on a glowing wave-shaped energy surface

These tutorials grew out of research on enzyme reaction mechanisms and enzyme-nanomaterial interfaces. Each one is a working protocol, with the inputs and scripts needed to reproduce it on your own system.

Alexandre V. Pinto, PhD in Chemistry

High Performance Computing in Molecular Modelling Research Group, LAQV-REQUIMTE

Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto

GitHub profile