liusfore

liusfore's Stars

• jsunn-y/ALDE

  Active Learning-Assisted Directed Evolution for Protein Engineering

  Language:Jupyter Notebook233

• Superzchen/iLearn

  iLearn, a Python Toolkit and Web Server Integrating the Functionality of Feature Calculation, Extraction, Clustering, Feature Selection, Feature Normalization, Dimension Reduction and Model Construction for Classification, Best Model Selection, Ensemble Learning and Result Visualization for DNA, RNA and Protein Sequences.

  Language:Python7731

• instadeepai/nucleotide-transformer

  🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

  Language:Python46354

• BorgwardtLab/proteinshake

  Protein structure datasets for machine learning.

  Language:Python1009

• lucidrains/alphafold3-pytorch

  Implementation of Alphafold 3 in Pytorch

  Language:Python1.1k128

• Graylab/MaskedProteinEnT

  Language:Python114

• wenjiegroup/ProMEP

  Zero-shot prediction of mutation effects on protein function with multimodal deep representation learning

  Language:Python395

• ikalvet/heme_binder_diffusion

  Language:Python8819

• ai4protein/ProSST

  Code for ProSST: A Pre-trained Protein Sequence and Structure Transformer with Disentangled Attention.

  Language:Python343

• oxpig/AntiFold

  Improved antibody structure-based design using inverse folding

  Language:Python7310

• dms-vep/SARS-CoV-2_Omicron_BA.2_spike_DMS

  Language:Jupyter Notebook1

• pinellolab/DNA-Diffusion

  🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

  Language:Python36252

• Eikor/InstructPLM

  The first large protein language model trained follows structure instructions.

  Language:Python675

• kyegomez/AlphaFold3

  Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

  Language:Python72595

• huggingface/lerobot

  🤗 LeRobot: Making AI for Robotics more accessible with end-to-end learning

  Language:Python6.9k625

• AspirinCode/awesome-AI4MolConformation-MD

  List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning

  11112

• westlake-repl/SaProt

  [ICLR'24 spotlight] Saprot: Protein Language Model with Structural Alphabet

  Language:Python33232

• salesforce/provis

  Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."

  Language:Python30148

• stebliankin/piston

  Evaluating Protein Binding Interfaces with Transformer Networks

  Language:Jupyter Notebook405

• EBI-Metagenomics/genomes-catalogue-pipeline

  MGnify genome analysis pipeline

  Language:Python10021

• y-hwang/gLM

  Genomic language model predicts protein co-regulation and function

  Language:Python658

• a96123155/UTR-LM

  Language:Jupyter Notebook6614

• lujiarui/Str2Str

  Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)

  Language:Python653

• da03/hierarchical_diffusion_LM

  Language:Python92

• TobiasHeOl/AbLang2

  An antibody-specific language model focusing on NGL prediction

  Language:Python114

• generatebio/chroma

  A generative model for programmable protein design

  Language:Python67789

• dakpinaroglu/Frame2seq

  Structure-conditioned masked language modeling for protein sequence design

  Language:Python586

• DeepRank/deeprank2

  An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.

  Language:Python3510

• bowang-lab/scGPT

  Language:Jupyter Notebook1k196

• chaitjo/geometric-rna-design

  gRNAde: Geometric Deep Learning for 3D RNA inverse design

  Language:Jupyter Notebook15014