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The Martinez Lab

Computational tools

We use a variety of computational tools in close integration with experimental techniques to understand protein function and behavior.

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Conformational changes in PAH
Photo:
Lars Skjærven

Computer-aided drug design

We make extensive use of protein-ligand docking to predict the binding modes of small molecule compounds in a three-dimensional model of the protein structure. High-throughput virtual screening allows the discrimination of binders and non-binders to a protein target. These in silico tools facilitates rapid inepxensive screening of large databases of compounds (thousands to millions of compounds).

 

Biomolecular simulations

Molecular dynamics simulations have an acknowledge capability to mimic in vitro conditions of isolated biomolecules (e.g. proteins), and can provide a complete picture of the dynamic and flexibility properties of protein structures.