Welcome to the 
van der vaart 
research group
DNA binding proteins

We are particularly interested in sequence specific DNA binding proteins.  Many DNA binding proteins fold upon binding their DNA target sequence, with some very interesting thermodynamic consequences.  We use large-scale molecular dynamics simulations to investigate the mechanism of coupled protein folding and DNA binding.

Method development

The main hurdle for the study of conformational changes by computer simulations is the time scale of the transitions.  We develop new techniques to enforce transitions in time scales accessible to molecular dynamics. We also develop new free energy simulation methods and analysis techniques for the study of conformational changes.

Drug design

We use molecular docking and other computational tools to design new drug leads for cancer and Alzheimer’s disease. Our work is in close collaboration with synthetic organic chemists and pharmacologists.
Biomolecular Simulations

Our research focuses on the conformational dynamics of proteins.  Proteins are not static molecules; most proteins change shape during and part of their functional cycle.  In fact, conformational changes are crucial for the proper functioning of many proteins.  Although their biological role is generally understood, insights into the microscopic origins of these changes are still lacking.  We aim to elucidate the fundamental principles responsible for the conformational behavior by a combination of existing and newly developed computational techniques. Dr. Arjan van der Vaart
Department of Chemistry
University of South Florida
4202 E Fowler Ave CHE 205
Tampa, FL 33620
Tel. 813-974-8762
Fax. 813-974-3230
Group members
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Department of Chemistry
City of Tampa
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