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

Metabolic Networks Quantification, Analysis and Redesign

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, 2018-09-24)

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)

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.

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)

FCF (2004): Flux Coupling Analysis

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

Protein Engineering

Protein-InDelMaker (Part of IPRO +/- package): an interactive Python package to make structural models of indel variants of proteins.

Rotamer library (input files for IPRO): a discrete set of statistically preferred conformations of side chains.

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)
Note: Please request short jobs using this google form

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.