Stars
List of papers about Proteins Design using Deep Learning
Neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data
A little guide to help you install & manage NVIDIA GPU driver on your Ubuntu system
Making RNA-based models accessible to all.
A playbook for systematically maximizing the performance of deep learning models.
Logic for running AlphaFold3 on an HPC cluster
Generation of protein sequences and evolutionary alignments via discrete diffusion models
A simple Snakemake profile for Slurm without --cluster-config
Biological foundation modeling from molecular to genome scale
enijkamp / progen2
Forked from salesforce/progenOfficial release of the ProGen models
A Nextflow workflow that utilizes GPU enabled Singularity containers to process scRNA-seq data
Inference code for PoET: A generative model of protein families as sequences-of-sequences
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures
🧬 Advanced hybrid language model for directed protein evolution. (NeurIPS 2024)
Saprot: Protein Language Model with Structural Alphabet (AA+3Di)
Open source code for AlphaFold 2.
New method to dectect recent positive selection by conditional coalescent tree (contact: wilyric[AT]gmail.com or minxian[AT]broadinstitute.org)
Slides and notebook from a 4 hour course aimed at incoming biology PhD students
nf-core pipeline for comparative analysis of ortholog predictions
A vim plugin to give you some slime. (Emacs)
Learning-Rate-Free Stochastic Riemannian Optimization in JAX.
The official code for "TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation"