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.
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-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.