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alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.

alphafold

Open source code for AlphaFold.

alphafold2

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

bio_embeddings

[WIP] python package to embed protein sequences using different models (contextualized and not)

colabfold

Making Protein folding accessible to all via Google Colab!

deepsequence-pytorch

egnn

gputil

A Python module for getting the GPU status from NVIDA GPUs using nvidia-smi programmically in Python

masif

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

meme

MEME motif-based sequence analysis tools (http://meme-suite.org), with FreeBSD tweaks

neurips19-graph-protein-design

Generative Models for Graph-Based Protein Design

openfold

Trainable PyTorch reproduction of AlphaFold 2

protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

tape-neurips2019

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

thermiagenesissmartcontrol

Smart control of Genesis heat pump based on electricity price

udsmprot

Protein sequence classification with self-supervised pretraining

uni-fold

uni-mol

A Universal 3D Molecular Representation Learning Framework