An object-oriented library for computational protein design

Arnab B. Chowdry, Kimberly A. Reynolds, Melinda S. Hanes, Mark Voorhies, Navin Pokala, Tracy M. Handel

Research output: Contribution to journalArticle

31 Scopus citations

Abstract

Recent advances in computational protein design have established it as a viable technique for the rational generation of stable protein sequences, novel protein folds, and even enzymatic activity. We present a new and object-oriented library of code, written specifically for protein design applications in C ++, called EGAD Library. The modular fashion in which this library is written allows developers to tailor various energy functions and minimizers for a specific purpose. It also allows for the generation of novel protein design applications with a minimal amount of code investment. It is our hope that this will permit labs that have not considered protein design to apply it to their own systems, thereby increasing its potential as a tool in biology. We also present various uses of EGAD Library: in the development of Interaction Viewer, a PyMOL plug-in for viewing interactions between protein residues; in the repacking of protein cores; and in the prediction of protein-protein complex stabilities.

Original languageEnglish (US)
Pages (from-to)2378-2388
Number of pages11
JournalJournal of Computational Chemistry
Volume28
Issue number14
DOIs
StatePublished - Nov 15 2007

Keywords

  • Computational protein design
  • Object-oriented programming
  • Protein stability
  • Protein-protein interactions

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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    Chowdry, A. B., Reynolds, K. A., Hanes, M. S., Voorhies, M., Pokala, N., & Handel, T. M. (2007). An object-oriented library for computational protein design. Journal of Computational Chemistry, 28(14), 2378-2388. https://doi.org/10.1002/jcc.20727