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

Enzymesin silico

Workflows, 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 Comparing protein pKa predictors to assign protonation states Run PROPKA3, PypKa, DelPhiPKa, pKAI and pKAI+ on the same protein structure, merge their pKa values into one table and assign protonation states at a target pH by consensus, with hen egg-white lysozyme (4LZT) as the worked example.

Portfolio

Open resources from my research in computational chemistry and biochemistry, from simulation workflows and force field parameters to structural models and software.

Showing all 11 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
  • Accepted conformers of MHET overlaid, with atoms coloured from red (negative) to blue (positive) by their ABCG2 charge

    Force fieldsNew

    Conformer-averaged ABCG2 charges

    Average ABCG2 partial charges over the conformers of a flexible molecule until the mean converges, with MHET as the worked example.

    Oct 2026
  • Lysozyme cartoon with the titratable side chains coloured from red (deprotonated) to blue (protonated) by their consensus pKa relative to pH 7, and the disulfide bonds in yellow

    Molecular dynamicsNew

    Comparing protein pKa predictors to assign protonation states

    Run PROPKA3, PypKa, DelPhiPKa, pKAI and pKAI+ on the same protein structure, merge their pKa values into one table and assign protonation states at a target pH by consensus, with hen egg-white lysozyme (4LZT) as the worked example.

    Oct 2026

Enzyme QM/MM with CP2K

  1. Preparing a QM/MM system
  2. Static QM/MM
  3. Dynamic QM/MM
  4. Per-residue contributions to the barrier
  5. Transition state macrodipole

About me

Portrait of Alexandre V. Pinto
An enzyme in pink and blue ribbons floating above a glossy free energy landscape of peaks and valleys

Alexandre V. Pinto, PhD in Chemistry

Researcher and invited assistant professor

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

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

Computational chemist working on enzyme catalysis. I use molecular dynamics and QM/MM methods to understand how enzymes work and to guide the design of better biocatalysts.

alexandre.pinto (at) fc.up.pt

Publications

  1. 2026

    Enhancing the catalytic performance of IsMHETase through electrostatic engineering of the active site

    K. S. R. Clausen, A. V. Pinto, R. Dorau, et al.

    Chem Circularity

  2. 2025

    Beyond Fang's fury: a computational study of the enzyme-membrane interaction and catalytic pathway of the snake venom phospholipase A2 toxin

    J. Castro-Amorim, A. V. Pinto, A. K. Mukherjee, M. J. Ramos, P. A. Fernandes

    Chemical Science

  3. 2024

    Revisiting the reaction pathways for phospholipid hydrolysis catalyzed by phospholipase A2 with QM/MM methods

    A. V. Pinto, P. Ferreira, A. V. Cunha, R. W. A. Havenith, A. L. Magalhães, M. J. Ramos, P. A. Fernandes

    Chemical Science

  4. 2023

    Development of nanoscale graphene oxide models for the adsorption of biological molecules

    A. V. Pinto, P. Ferreira, P. A. Fernandes, A. L. Magalhães, M. J. Ramos

    The Journal of Physical Chemistry BFront cover

  5. 2022

    The role of acetylated cyclooxygenase-2 in the biosynthesis of resolvin precursors derived from eicosapentaenoic acid

    A. Cebrián-Prats, A. V. Pinto, À. González-Lafont, P. A. Fernandes, J. M. Lluch

    Organic & Biomolecular Chemistry

  6. 2021

    Reaction mechanism of MHETase, a PET degrading enzyme

    A. V. Pinto, P. Ferreira, R. P. P. Neves, P. A. Fernandes, M. J. Ramos, A. L. Magalhães

    ACS CatalysisFront cover

  7. 2020

    Intramolecular hydrogen bonds in tip-functionalized single-walled carbon nanotubes as pH-sensitive gates

    A. V. Pinto, A. L. Magalhães

    The Journal of Physical Chemistry A

Journal covers and artwork

  • Front cover of ACS Catalysis, Volume 11, issue 16 (2021) Volume 11, issue 16 (2021)
  • Front cover of Nature Reviews Chemistry, Volume 6, issue 7 (2022) Volume 6, issue 7 (2022)
  • Front cover of The Journal of Physical Chemistry B, Volume 127, issue 2 (2023) Volume 127, issue 2 (2023)
  • Human phospholipase A2 in magenta ribbons inside a white surface, resting on a membrane surrounded by water molecules and ions Human sPLA2 at a membrane
  • MHETase in pink and white ribbons, surrounded by a blurred halo of coloured copies of its structure MHETase
  • Snake venom phospholipase A2 in yellow ribbons and a pink surface, sitting on a lilac lipid membrane with a phospholipid drawn into its active site Bothrops asper sPLA2 at a membrane
  • Human phospholipase A2 in glowing pink ribbons, with a phospholipid in white spheres in its active site Human sPLA2 and a phospholipid
  • Grey molecular surface of MHETase on a graphene oxide sheet covered by water molecules MHETase on graphene oxide