Protein Structure Modelling and Design
RESEARCH
The aim of our group is to better understand how biology acts at the molecular level, how proteins behave dynamically, how these molecules recognize one another and their cognate ligands and/or proteins. In this ambit, we conduct computational protein structural analysis, prediction, redesign and engineering in order to infer the molecular function of proteins, to develop novel therapeutic agents and to improve the properties of existing ones.
We are also interested in the development of new methodologies for structure prediction, new methods for assessing the reliability of structural models, new methods for structure based function prediction, as well as in modelling, engineering and redesign of proteins of biomedical interest.
WHO WE ARE
PROJECTS
The Protein Structure Modelling and Design Group has extensive collaborations with many groups.
Actual projects and/or collaborations:
- ENCODE
pilot phase in collaboration with the Biosapiens Network of
excellence (EU). In this ambit we
are performing a fully automatic pipeline for protein structure
modelling and evaluation.
- Dynamical and functional studies on cytokine-like proteins in collaboration with BioKer. Several proteins are being studied with the aim of designing therapeutic molecules.
- Large-scale flexible protein-protein docking.
Our principal aim is to include backbone flexibility in the docking protocols.
COMPUTATIONAL TOOLS
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Protein dynamical properties: We perform the Molecular Dynamics simulations using GROMACS and NAMD workpackages
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Flexible protein-protein docking: We are carring out protein-protein docking experiments on experimentally verified systems using normal modes calculations to infer flexibility, together with Rosetta-Dock
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Protein Modelling and Design: We use state of art structure modelling programs and algorithms, such as, Modeller 9v2, HHpred, Rosetta, mGenthreader and others, depending on the difficulty of each of the particular cases.