Software

All software is licensed under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
× We have recently published a book that provides tutorial on various computational tools developed for the analysis of metabolic network. Check out our book website and GAMS code in GitHub !
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If you have a general question concerning the website or any problems with download, please contact the webmaster ( lqw5322@psu.edu).

A simple tutorial for running GAMS code (i.e. file with .gms extension) is provided here.

Metabolic Networks Quantification, Analysis and Redesign

BiomassMW (2017): Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models. (Last updated, 2017-08-96)

SteadyCom (2017): Predicting microbial abundances while ensuring community stability. (Last updated, 2017-07-26)

Precursor Identifier (2015): Identify biomass precursors that are not produced upon essential (synthetic lethal) gene deletion. (Last updated, 2016-05-26)

CLCA (2014): Maximum Common Molecular Substructure Queries within the MetRxn Database. (Last updated, 2016-05-22)

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

OptForce (2010): Identify the minimal set of genetic interventions that shape the metabolism of a microorganism. (Last updated, 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

PoreDesigner (2018): an novel tool using the IPRO suite of programs that is capable of engineering constriction region of beta-barrel (and also alpha-helical) proteins to any desired pore size and make it hydrophobic (Last updated, 2018-07-03)
HUMANIZER (2018): in silico affinity maturation of murine or de novo designed antibodies that not only enhances binding affinity to the specific antigen epitope, but also make them more humanized (Last updated, 2018-06-18)

OptMAVEn_2.0 (2018): Automated tool for de novo design of humanized monoclonal antibody variable regions targeting a specific antigen epitope (Last updated, 2018-06-18)

AOM_Bottleneck_Inputs (2018): Input file for AOM_Bottleneck (Last updated, 2018-06-16)

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

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

OptZyme (2013): Enzyme redesign through the use of transition state analogues. (Last updated, 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.