Research

See "Software" section for software distribution

OVERVIEW

Our research addresses biological and medical challenges from single molecules to the genome with high performance computing and theory. Specific areas of research include protein-ligand interactions for drug discovery, RNA structure prediction and biomaterials design. In collaboration with other experimental groups, we utilize computer modeling and simulations to understand these complex biomolecular systems and to discover molecules for treating disease and improving human health.

In the areas of software development, we are contributors to molecular modeling software TINKER and AMBER. Our physical models (polarizable force fields) are also available through FFX and OpenMM.

_______________________________________________________________

DRUG DISCOVERY

Supported by CIPRIT, we are part of The Targeted Therapeutic Drug Discovery & Development Program (TTDDDP) (http://sites.utexas.edu/ttdddp/).

___________________________________________________________

PROTEIN-LIGAND BINDING

We are interested in understanding the molecular driving forces for protein-ligand recognition using modeling and simulations, and developing novel molecular probes and therapeutics.

Simulation movie: http://biomol.bme.utexas.edu/~pren/multimedia/movie/youtube/trypsin-osrw...

Working with Prof. Kevin Dalby in Med Chem, UT School of Pharmacy, we are examining proteins in the MAPK signaling pathway, which is involved in abnormal cell proliferation, apoptosis and resistance to cancer therapy. Our work helps understand how these proteins work and develop novel inhibitors and drug candidates.

movie on cell MAPK signaling.

_____________________________________________________________

COMPUTATIONAL MODELING AND SOFTWARE DEVELOPMENT

One of our main research directions is to develop cutting edge physical models and software for molecular modeling and design. We develop force fields for proteins and other biomolecules that enable us to accurately predict biomolecular structures and interactions in silico. This effort is in collaboration with Jay Ponder (Wash Univ), Jean-Philips Piquemal (Univ Paris), Andreas Cisneros (Wayne State), Mike Schnieders (Univ. Iowa) and Wei Yang (Florida State Univ).

_____________________________________________________________

MULTISCALE MODELING of RNAs

Folding of U2/U6 snRNA using a coarse-grained model developed in the lab:

Click here for Simulation movie   

_____________________________________________________________

CRYSTAL STRUCTURE & PROPERTY PREDICTION

Simulation of Aspirin crystal structure: http://biomol.bme.utexas.edu/~pren/multimedia/movie/youtube/aspirin-crys...

_____________________________________________________________

SELF-ASSEMBLY MATERIALS

In collaboration with Prof. Laura Suggs of UT BME, we study the self-assembly mechanism of Fmoc-AA fibril and develop new mimetics for tissue engineering applications.

Simulation movie: http://biomol.bme.utexas.edu/~pren/multimedia/movie/youtube/Fmoc-AA-SA3.mp4