Research Line
Biophysics of ion channels
Molecular dynamics and free-energy approaches applied to ion channels and other membrane proteins. We characterise gating, permeation and drug binding in atomistic detail, and translate it into ligand design and selectivity predictions for neurological, cardiac and metabolic targets.
What we work on
Specific simulation and modelling problems we tackle for in-house projects and external collaborations.
- All-atom molecular dynamics of ion channels and transporters in explicit lipid bilayers (GROMACS, Desmond, AMBER).
- Binding-energy calculations with MM/GBSA, MM/PBSA and selected free-energy perturbation protocols.
- Selectivity profiling of compounds across related channel subtypes (cardiac, neuronal, glial).
- Allosteric and lipid-mediated modulation studies for novel binding sites.
- Membrane-protein modelling when crystal structures are unavailable — homology, AlphaFold-derived and refined models.
Tools we use
- TOLEDO — batch execution of Maestro-Desmond molecular dynamics on HPC.
- ASGARD — automated MD analysis and reporting for GROMACS simulations.
- MetaScreener — virtual screening with subsequent MD-based refinement.
Applications & target areas
Therapeutic areas where ion-channel modulation is central — and where we can run simulations and design ligands for partners.
NeurologySodium, potassium and calcium channels relevant to epilepsy, pain and neurodegeneration.
CardiologyCardiac potassium channels (hERG and others) — both for safety filtering and as therapeutic targets.
MetabolismChannels and transporters involved in insulin secretion and energy homeostasis.
Membrane-protein modellingGPCRs, kinases and transporters where MD is required for accurate binding prediction.
Selected resources
- ASGARD — automated MD analysis (GROMACS) — DOI 10.1080/07391102.2024.2349527
- TOLEDO — batch Maestro-Desmond MD on HPC — DOI 10.1080/07391102.2024.2423380
Interested in this line?
Contact Prof. Horacio Pérez-Sánchez · hperez@ucam.edu