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.
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-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)