Official git repository for Biopython (originally converted from CVS)
- python
- bioinformatics
- genomics
- biopython
Repository Index
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Official repository for the Boltz biomolecular interaction models
- binding-prediction
- drug-discovery
- protein-structure
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
- pytorch
- protein-structure
- alphafold2
Code for the ProteinMPNN paper
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
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
Official release of the ProGen models
- language-model
- protein
- generative-model
Generation of protein sequences and evolutionary alignments via discrete diffusion models
- discrete-diffusion
- generative-model
- multiple-sequence-alignment
- protein-sequences
OmegaFold Release Code
A Python Package for Protein Dynamics Analysis
- python
- protein
- dynamics
Generative biopolymer design with rich conditioning.
Official repository for the ProteinGym benchmarks
- benchmark
- computational-biology
- protein
- protein-design
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
A collection of research papers for AI-based protein design
Source code for "DeepDTA: deep drug-target binding affinity prediction"
- protein-ligand-interactions
- convolutional-neural-networks
Ankh: Optimized Protein Language Model
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
We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.
- ai-aided-drug-discovery
- awesome
- drug-discovery
- molecular-docking
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"
Human Protein Atlas image classification competition