TY - JOUR
T1 - The Iterative Protein Redesign and Optimization (IPRO) suite of programs
AU - Pantazes, Robert J.
AU - Grisewood, Matthew J.
AU - Li, Tong
AU - Gifford, Nathanael P.
AU - Maranas, Costas D.
N1 - Publisher Copyright:
© 2014 Wiley Periodicals, Inc.
PY - 2015/2/5
Y1 - 2015/2/5
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/84920861353
UR - https://www.scopus.com/inward/citedby.url?scp=84920861353&partnerID=8YFLogxK
U2 - 10.1002/jcc.23796
DO - 10.1002/jcc.23796
M3 - Article
C2 - 25448866
AN - SCOPUS:84920861353
SN - 0192-8651
VL - 36
SP - 251
EP - 263
JO - Journal of Computational Chemistry
JF - Journal of Computational Chemistry
IS - 4
ER -