Welcome to the

van der vaart

research group


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



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.

Bacteriological toxins

Certain bacteriological toxins undergo large conformational changes as part of their activation mechanism.  We aim to uncover the interactions responsible for the motion by modeling techniques and computer simulations, which will aid our design of ligands to block the motion.


Kinases are crucial in cell signaling pathways and are often involved in cancer. We perform simulations to further the understanding of their conformational activation mechanism.

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.

Group members