*** The software download site is temporarily unavailable. Please contact auk241@psu.edu. ***

Metabolic Networks Quantification, Analysis and Redesign

OptCom (2012): A comprehensive modeling framework for the flux balance analysis of microbial communities. (New, 2012-10-08)

OptForce (2010): Identifies the minimal set of genetic interventions that shape the metabolism of a microorganism. (New, 2011-11-15)

SL Finder (2009): Identify synthetic lethal genes or reactions in genome-scale metabolic models.

EMU generator (2009): Elementary Metabolite Unit generation code for isotope mapping models. (Last updated 2014-12-01)

GrowMatch (2009): Reconciling in silico predictions with in vivo growth observations. (Last updated 2011-07-14)

GapFind/GapFill (2007): Identifying and filling network gaps for genome-scale metabolic models. (Last updated 2011-09-23)

FCF (2004): Flux Coupling Analysis

OptKnock (2003): Strain redesign for overproduction using gene/reaction deletions. (Last updated 2011-11-01)

Protein Engineering

IPRO Suite of Programs: (2014): Integrated environment for various protein engineering tasks (New, 2014-10-12)

MAPs (2013): A database of Modular Antibody Parts for predicting and designing antibody variable domains (New, 2013-05-29)

OptZyme (2013): Enzyme redesign through the use of transition state analogues. (New, 2013-05-16)

OptCDR (2010): De novo design of antibody Complementarity Determining Regions for binding targeted epitopes in antigens.

IPRO (2006): Iterative Protein Redesign and Optimization.
(last updated 2009-07)

eShuffle (2001): Prediction of crossover distributions using DNA shuffling.