In Silico Design of Smart Binders to Anthrax PA
ARMY RESEARCH LAB ABERDEEN PROVING GROUND MD WEAPONS AND MATERIALS RESEARCH DIRECTORATE
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The development of smart peptide binders requires an understanding of the fundamental mechanisms of recognition which has remained an elusive grail of the research community for decades. Recent advances in automated discovery and synthetic library science provide a wealth of information to probe fundamental details of binding and facilitate the development of improved models for a priori prediction of affinity and specificity. Here we present the modeling portion of an iterative experimentalcomputational study to produce high affinity peptide binders to the Protective Antigen PA of Bacillus anthracis. The result is a general usage, HPC-oriented, python-based toolkit based upon powerful third-party freeware, which is designed to provide a better understanding of peptide-protein interactions and ultimately predict and measure new smart peptide binder candidates. We present an improved simulation protocol with flexible peptide docking to the Anthrax Protective Antigen, reported within the context of experimental data presented in a companion work.
- Anatomy and Physiology
- Medicine and Medical Research
- Computer Programming and Software