enzyme-design

The Rosetta Bio-macromolecule modeling package. Available through license with the University of Washington.

Code for the DISCO model: General Multimodal Protein Design Enables DNA-Encoding of Chemistry

Scripts for converting Rosetta enzyme design constraint files into regular Rosetta constraint files

The new and improved server combining Pedel, Mutanalyst and much more

Extract, structure, and apply visual design identity as machine-readable Design DNA across tokens, style, and effects

De novo enzyme design of oxirane:NAD(P)H reductase enzyme

BioBrigit: Hybrid machine learning and knowledge-based approach for the prediction of metal diffusion pathways through proteins

EnzyOrchestra: OSS cross-generator in-silico validation harness for de novo enzyme design. Orchestrates RFdiffusion2/ProHiFlo/AgentPLM with catalytic-specific metrics (dG, solubility, CAI). Method-independent, AGPL-3.0-or-later.

This repo contains the data from: EVCouplings, DynaMut2, MDM-TASK, MD simulation. These files are important for understanding book chapter 17 "Computational Methods to Engineer Cas Proteins for Efficient Genome Editing"

A robust and scalable framework for resource-constraint models through stochastic tuning of deep learning-predicted kinetic parameters

Reproducible de novo dicopper PPO design workflow with theozyme inputs, sampling, scoring, review, and FASTA delivery

Tools for enzyme engineers

De novo design of hydratase, aromatic edition

Code and raw data for my paper "Biocatalytic conversion of ethylene…"

What Is Enzyme Kinetics is a Python toolkit for enzyme kinetics, Michaelis-Menten fitting, reaction-rate equations, parameter prediction, inhibition and dose-response analysis. Explore enzyme activity, substrates, catalytic models, BRENDA data parsing, time-course processing and reproducible kinetic simulations.

Enzymit — independent third-party profile of a public API surface, by API Evangelist. Enzymit is a synthetic biology company based in Rehovot, Israel that designs novel enzymes and enables cell-free biomanufacturing. Its proprietary platform combines computational protein design, deep learning, and high-throughput testing to develop enzymes for bio