maranasgroup

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42 repositories

CatPred
Public
Machine Learning models for in vitro enzyme kinetic parameter prediction
deep-learning ml regression python3 pytorch enzyme-kinetics protein-property-prediction
Python
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MIT License
•1•19•1•0•Updated Jan 17, 2025Jan 17, 2025
Protein-InDelMaker
Public
A Rosetta-based Python tool for constructing user-defined variant libraries with amino acid insertions, deletions, using loop closure algorithms and energy minimization.
numpy protein-structure python3 pyrosetta
Python
•1•3•0•0•Updated Jan 17, 2025Jan 17, 2025
chemo-enz
Public
Expanding chemical synthesis planning to explore chemo-enzymatic pathways using minimal transitions
Jupyter Notebook
•0•0•0•0•Updated Jan 13, 2025Jan 13, 2025
novoStoic2.0
Public
novoStoic2.0: Integrated Pathway Design Tool with Thermodynamic Considerations and Enzyme Selection
Jupyter Notebook
•7•8•0•0•Updated Aug 23, 2024Aug 23, 2024
KETCHUP
Public
Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP)
Python
•0•1•0•0•Updated Jun 28, 2024Jun 28, 2024
optstoic-gams
Public
optStoic-minFlux/minRxn code for PMID: 26530953
GAMS
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Apache License 2.0
•2•0•0•0•Updated Apr 25, 2024Apr 25, 2024
CatPred-DB
Public
Python
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MIT License
•0•0•1•0•Updated Apr 11, 2024Apr 11, 2024
iSace_GSM
Public
Repository of a genome-scale metabolic model for Saccharomyces cerevisiae
metabolism yeast constraint-based-modeling metabolic-model saccharomyces-cerevisiae
Jupyter Notebook
•1•0•0•0•Updated Mar 11, 2024Mar 11, 2024
yeastsMFA
Public
Repository for yeasts MFA related files
metabolism metabolic-flux-analysis
MATLAB
•1•2•0•0•Updated Mar 11, 2024Mar 11, 2024
iPotri3463
Public
This repository contains multi-tissue metabolic models of populus trichocarpa
Jupyter Notebook
•1•0•0•0•Updated Feb 15, 2024Feb 15, 2024
dGPredictor
Public
Jupyter Notebook
•2•10•1•1•Updated Dec 15, 2023Dec 15, 2023
iCTH669
Public
Repository for the Stoichiometric Genome-Scale Model (GSM) of Clostridium thermocellum
HTML
•0•3•0•0•Updated Oct 11, 2023Oct 11, 2023
CNN_seq_CoV2
Public
Python
•0•1•0•0•Updated Sep 28, 2023Sep 28, 2023
scRBA
Public
S. cerevisiae Resource Balance Analysis model
metabolism flux-balance-analysis constraint-based-modeling resource-balance-analysis
GAMS
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MIT License
•2•1•0•0•Updated Jun 8, 2023Jun 8, 2023
EnzRank
Public
PureBasic
•2•3•0•0•Updated May 18, 2023May 18, 2023
iRhto_memote
Public
Memote-created repository for Rhodosporidium toruloides model iRhto
metabolism yeast constraint-based-modeling metabolic-model
HTML
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Creative Commons Attribution 4.0 International
•3•0•0•0•Updated Mar 1, 2023Mar 1, 2023
k-sacce306
Public
K-FIT kinetic models for Saccharomyces cerevisiae CEN.PK and BY4741
MATLAB
•2•0•0•0•Updated Dec 22, 2022Dec 22, 2022
kcat-km
Public
Predictive models for estimating kcat and km of enzymes from sequence/structure information
Python
•1•3•0•0•Updated Nov 14, 2022Nov 14, 2022
SNPeffect
Public
Python
•0•1•0•0•Updated Feb 24, 2022Feb 24, 2022
k-ctherm138
Public
MATLAB
•0•1•0•0•Updated Feb 7, 2022Feb 7, 2022
ensembledocking
Public
Codes for ensemble docking
0•0•0•0•Updated Jan 10, 2022Jan 10, 2022
SteadyState-MFA
Public
Genome scale steady state 13C metabolic flux analysis
MATLAB
•3•2•2•0•Updated Nov 30, 2021Nov 30, 2021
uncFBA
Public
metabolism uncertainty-propagation flux-balance-analysis constraint-based-modeling
Jupyter Notebook
•1•1•0•0•Updated Nov 2, 2021Nov 2, 2021
dGPredictor-py2
Public
Jupyter Notebook
•
GNU General Public License v3.0
•1•2•2•1•Updated Aug 9, 2021Aug 9, 2021
K-FIT
Public
MATLAB
•2•1•0•0•Updated Jul 19, 2021Jul 19, 2021
NN_MM-GBSA_CoV2
Public
Python
•1•6•0•0•Updated Mar 26, 2021Mar 26, 2021
DMMM
Public
Dynamic multi-species metabolic modeling of Clostridia co-culture
MATLAB
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MIT License
•0•0•0•0•Updated Feb 23, 2021Feb 23, 2021
UCYN-A-symbiosis-metabolic-modeling
Public
GAMS
•1•0•0•0•Updated Feb 9, 2021Feb 9, 2021
iIsor_memote
Public
Repository for Issatchenkia orientalis SD108 genome-scale metabolic model iIsor
Other
•1•0•0•0•Updated Feb 5, 2021Feb 5, 2021
optstoic-python
Public
Jupyter Notebook
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MIT License
•4•3•0•2•Updated Aug 22, 2020Aug 22, 2020