Repository Index

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

• pytorch
• protein-structure
• alphafold2

Code for the ProteinMPNN paper

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

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

Generation of protein sequences and evolutionary alignments via discrete diffusion models

• discrete-diffusion
• generative-model
• multiple-sequence-alignment
• protein-sequences

OmegaFold Release Code

Official repository for the ProteinGym benchmarks

• benchmark
• computational-biology
• protein
• protein-design

Source code for "DeepDTA: deep drug-target binding affinity prediction"

• protein-ligand-interactions
• convolutional-neural-networks

LLM for Drug Editing, ICLR 2024

• chatgpt
• conversation
• drug
• drug-discovery

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

• protein
• protein-sequences
• protein-design
• representation-learning

Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.

• alphafold3
• docking
• drug-design
• drug-discovery

PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"