Python Proteins Resources

Protein GLM (wip) Implementation of a protein autoregressive language model, but with autoregressive infilling objective (editing subsequences capabil

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

NNR and global probabilities estimation and analysis in peptides or protein fragments This module calculates global and NNR conformation dependent pro

Evolutionary Scale Modeling This repository contains code and pre-trained weights for Transformer protein language models from Facebook AI Research, i

A geometric deep learning pipeline for predicting protein interface contacts.

ProGen - (wip) Implementation and replication of ProGen, Language Modeling for Protein Generation, in Pytorch and Jax (the weights will be made easily

ProteinBERT is a universal protein language model pretrained on ~106M proteins from the UniRef90 dataset. Through its Python API, the pretrained model can be fine-tuned on any protein-related task in a matter of minutes. Based on our experiments with a wide range of benchmarks, ProteinBERT usually achieves state-of-the-art performance. ProteinBERT is built on TenforFlow/Keras.

Differentiable molecular simulation of proteins with a coarse-grained potential This repository contains the learned potential, simulation scripts and