The Iterative Protein Redesign and Optimization (IPRO) suite of programs

Robert J. Pantazes, Matthew J. Grisewood, Tong Li, Nathanael P. Gifford, Costas D. Maranas

Research output: Contribution to journalArticlepeer-review

32 Scopus citations

Abstract

Proteins are an important class of biomolecules with applications spanning across biotechnology and medicine. In many cases, native proteins must be redesigned to improve various performance metrics by changing their amino acid sequences. Algorithms can help sharpen protein library design by focusing the library on sequences that optimize computationally accessible proxies. The Iterative Protein Redesign and Optimization (IPRO) suite of programs offers an integrated environment for (1) altering protein binding affinity and specificity, (2) grafting a binding pocket into an existing protein scaffold, (3) predicting an antibody's tertiary structure based on its sequence, (4) enhancing enzymatic activity, and (5) assessing the structure and binding energetics for a specific mutant. This manuscript provides an overview of the methods involved in IPRO, input language terminology, algorithmic details, software implementation specifics and application highlights. IPRO can be downloaded at http://maranas.che.psu.edu.

Original languageEnglish (US)
Pages (from-to)251-263
Number of pages13
JournalJournal of Computational Chemistry
Volume36
Issue number4
DOIs
StatePublished - Feb 5 2015

All Science Journal Classification (ASJC) codes

  • General Chemistry
  • Computational Mathematics

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