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 !

If you have a general question concerning the website or any problems with download, please contact the webmaster (Wheaton L. Schroeder).

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

Metabolic Networks Quantification, Analysis and Redesign

dGPredictor (2021): dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. (Last updated, 2021-04-12)

SNPeffect (2020): SNPeffect: Automated identification of functional roles of SNPs using metabolic networks. (Last updated, 2022-02-22)

K-FIT (2019): K-FIT for kinetic model parameter estimation. (Last updated, 2019-07-17)

rePrime and novoStoic (2019): Pathway synthesis using de novo steps through uncharted biochemical spaces. (Last updated, 2019-05-29)

optStoic_v2 (2019): Designing overall stoichiometric conversions and intervening metabolic reactions (python version). (Last updated, 2019-01-01)

Nonstationary-MFA (2018): Nonstationary 13C metabolic flux analysis at a genome-scale. (Last updated, 2018-09-24)

SteadyState-MFA (2015): Steady state 13C metabolic flux analysis at a genome-scale. (Last updated, 2019-11-18)

BiomassMW (2017): Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models. (Last updated, 2017-08-26)

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

optStoic (2015): Designing overall stoichiometric conversions and intervening metabolic reactions. (Last updated, 2015-12-30)

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.(Last updated 2011-08-17)

EMU generator (2015): 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)

FCA (2004): Flux Coupling Analysis (Last updated 2004-03-15)

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

Protein Engineering

Protein-InDelMaker (2021, Part of IPRO +/- package): an interactive Python package to make structural models of indel variants of proteins (Last updated, 2021-01-27)

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)

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)
Note: Please request short jobs using this google form

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

Rotamer library (2016, input files for IPRO): a discrete set of statistically preferred conformations of side chains (Last updated, 2016-07-20)

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.(last updated 2010-05-10)

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

eShuffle (2001): Prediction of crossover distributions using DNA shuffling.(last updated 2002-04-24)