Computational Chemistry & Molecular Modeling Group

3D Structures & Tool Development

Lee G. Pedersen, Ph.D.
Principal Investigator

Tel (919) 541-4630
Fax (919) 541-0779
pederse3@niehs.nih.gov P.O. Box 12233
Mail Drop F0-08
Research Triangle Park, North Carolina 27709
Delivery Instructions

Research Summary

The Computational Chemistry & Molecular Modeling Group serves two major roles:

1. To assist other NIEHS scientists in understanding structural, mutational and sequence data that they generate using a variety of tools, such as graphics, energy minimization, simulations, relative free energy and homology-structure.
2. To develop new tools to overcome barriers so that the needs, in the context of the Institute, can be accommodated.

Three-dimensional structures are currently being generated at an exponential rate from experimental laboratories that focus on structure determination—X-ray, electron crystallography and NMR spectroscopy. Likewise, one-dimensional sequences of proteins and nucleic acids are appearing, also at an exponential rate. The appearance of sequences, however, is at a faster rate. The task, then, is to use the smaller data base (3D) to estimate 3D structures for molecules in the larger data base (1D).

Major areas of research:

• The development of new tools to aid understanding of structural, mutational and sequence data
• Modeling of DNA Polymerases (beta, lambda and epsilon, HIV Reverse transcriptases), calcium channels, DNA helicases, protein complexes in blood coagulation cascade, Sulfotransferases

Current projects:

• Drug polymorphism predictions
• Metal ion specificities
• Advanced force field for QM/MM applications
• Massively parallel MD simulations
• Transition Path Sampling (Metadynamics)
• Determination of reaction mechanism of Polymerase-lambda by QM/MM methods

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