Pinned Repositories
bagel-project
How to build a large dataset of enzyme variants to evaluate enzyme design algorithms
bglb_family
Quantitative prediction of mutant function across an enzyme family
cribbage
AI-powered cribbage for your command line
enzyme_design_constraint_converter
Scripts for converting Rosetta enzyme design constraint files into regular Rosetta constraint files
gato
Protein design using graph attention networks (GATs)
heme
Fast and friendly tools for protein design
protein-sedd
Based on: Lou+ [ICML 2024 Best Paper] Discrete Diffusion Modeling by Estimating the Ratios of the Data Distribution (https://arxiv.org/abs/2310.16834)
protein-transformers
Use generative ML to design new proteins using this simple, hackable implementation of protein transformer models
protein-transformers-from-scratch
Video lecture series on building generative ML models for protein sequences from scratch
dacarlin's Repositories
dacarlin/boxi
De novo enzyme design of oxirane:NAD(P)H reductase enzyme
dacarlin/kunkel-app
Internal web app for Kunkels
dacarlin/michaelis_menten_fitter
Example iPython notebook showing how to fit experimental data to the Michaelis-Menten equation
dacarlin/gs-checker
Automatic sequence verifier for Kunkel mutagenesis
dacarlin/angie
dacarlin/bagel-data
Published data and exploratory data visualizations for the Bagel project
dacarlin/bagel-draft
Draft of first Bagel paper reporting kinetics for 103 mutants
dacarlin/bagel-kinetics
Analysis of kinetic data from Bagel project
dacarlin/bagel-learn
Playground for modeling and machine learning for the Bagel project
dacarlin/bagel-model
Improved modelling for the Bagel project
dacarlin/bagel-thermostability
Repository of data and data tools for enzyme thermal stability data
dacarlin/blind-searcher
A blind searching algorithm for systematically preturbing protein sequence during design simulations
dacarlin/carlin_cookbook
Carlin Family Cookbook
dacarlin/cm_server
Siegel Lab comparative modeling server
dacarlin/cookbook
Protocols for common lab tasks in cookbook format
dacarlin/de_novo_hydratase
dacarlin/dnh
De novo design of hydratase
dacarlin/example_site
Example web site hosted on GitHub pages
dacarlin/hydratase
Rosetta model of oleate hydratase
dacarlin/ichp
iChip
dacarlin/mdh
dacarlin/one-pot
dacarlin/orders
Automated ordering of Kunkel mutagenesis on Transcriptic
dacarlin/oxbowventures.com
Static website for Oxbow Ventures
dacarlin/pick-a-place
Pick a place for lunch in Davis, California
dacarlin/point-scan
dacarlin/sequencing
Automated results from Kunkel sequencing
dacarlin/shaker-rack
Rack for two dozen 50 mL Falcon tubes that will fit any shaker
dacarlin/ssdna
Prototype of ssDNA prep on Transcriptic
dacarlin/wouhowe.com