alphafold2

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

🧬 gget enables efficient querying of genomic reference databases

User friendly and accurate binder design pipeline

Optimizing AlphaFold Training and Inference on GPU Clusters

Saprot: Protein Language Model with Structural Alphabet (AA+3Di)

Trainable PyTorch framework for developing protein, RNA and complex models.

Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

Trainable AlphaFold implementation in JAX

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

MMseqs2 app to run on your workstation or servers

Protein 3D structure prediction pipeline

Exploring Evolution-aware & free protein language models as protein function predictors

Local Interaction Score (LIS) Calculation from AlphaFold-Multimer (Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer)

FrameDiPT: an SE(3) diffusion model for protein structure inpainting

A curated list of awesome self-learning materials in Computational Structural Biology, such as sources, tutorials, etc.

Run AlphaFold2 (and multimer) step by step

A C, C++, Python project focusing on Docking analysis, Source code, Blogs, Data availability, References.

Cryptic pocket prediction using AlphaFold 2

Infrastructure template and Jupyter notebooks for running RoseTTAFold on AWS Batch.