Alternatives and similar repositories for OntoProtein

Users that are interested in OntoProtein are comparing it to the libraries listed below

• DeepGraphLearning / ProtST
  [ICML-23 ORAL] ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts
  ☆98Updated last year
• QizhiPei / BioT5
  BioT5 (EMNLP 2023) and BioT5+ (ACL 2024 Findings)
  ☆117Updated last year
• HICAI-ZJU / KANO
  Code and data for the Nature Machine Intelligence paper "Knowledge graph-enhanced molecular contrastive learning with functional prompt".
  ☆129Updated last year
• blender-nlp / MolT5
  Associated Repository for "Translation between Molecules and Natural Language"
  ☆186Updated 2 years ago
• zjunlp / NLP4SciencePapers
  Must-read papers on NLP for science.
  ☆58Updated 2 years ago
• ProtLLM / ProtLLM
  [ACL 2024] ProtLLM: An Interleaved Protein-Language LLM with Protein-as-Word Pre-Training
  ☆49Updated last year
• QizhiPei / Awesome-Biomolecule-Language-Cross-Modeling
  Awesome-Biomolecule-Language-Cross-Modeling: a curated list of resources for paper "Leveraging Biomolecule and Natural Language through M…
  ☆226Updated 5 months ago
• DeepGraphLearning / PEER_Benchmark
  PEER Benchmark, appear at NeurIPS 2022 Dataset and Benchmark Track (https://arxiv.org/abs/2206.02096)
  ☆95Updated 2 years ago
• zjunlp / MolGen
  [ICLR 2024] Domain-Agnostic Molecular Generation with Chemical Feedback
  ☆176Updated 9 months ago
• lvguofeng / GNN_PPI
  Codes and models for the paper "Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction".
  ☆82Updated 3 years ago
• elttaes / Revisiting-PLMs
  Exploring Evolution-aware & free protein language models as protein function predictors
  ☆63Updated last year
• THUDM / ProteinLM
  Protein Language Model
  ☆119Updated last year
• KyGao / ABGNN
  PyTorch code for KDD 2023 paper "Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design"
  ☆53Updated last year
• zqgao22 / HIGH-PPI
  ☆90Updated 2 years ago
• linjc16 / Pisces
  [RECOMB 2023] Official implementation of "Pisces: A combo-wise contrastive learning approach to synergistic drug combination prediction".
  ☆14Updated last year
• wengong-jin / RefineGNN
  ☆130Updated 3 years ago
• thunlp / KV-PLM
  Source code for "A Deep-learning System Bridging Molecule Structure and Biomedical Text with Comprehension Comparable to Human Profession…
  ☆90Updated 2 years ago
• peizhenbai / DrugBAN
  Interpretable bilinear attention network with domain adaptation improves drug-target prediction.
  ☆128Updated 2 years ago
• zjunlp / Mol-Instructions
  [ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models
  ☆285Updated 11 months ago
• QizhiPei / SSM-DTA
  SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction (Briefings in Bioinformatics 2023)
  ☆53Updated last year
• DeepGraphLearning / GearNet
  GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)
  ☆299Updated 3 months ago
• mmcdermott / structure_inducing_pre-training
  ☆16Updated 3 years ago
• chao1224 / ProteinDT
  A Text-guided Protein Design Framework, Nat Mach Intell 2025 (https://www.nature.com/articles/s42256-025-01011-z)
  ☆94Updated 8 months ago
• OmicsML / awesome-molecule-protein-pretrain-papers
  ☆45Updated last year
• hadi-abdine / Prot2Text
  ☆39Updated 3 months ago
• Fangyinfff / KCL
  Code and Data for the paper: Molecular Contrastive Learning with Chemical Element Knowledge Graph [AAAI 2022]
  ☆90Updated last year
• chao1224 / GraphMVP
  Pre-training Molecular Graph Representation with 3D Geometry, ICLR'22 (https://openreview.net/forum?id=xQUe1pOKPam)
  ☆198Updated 3 years ago
• lsj2408 / Transformer-M
  [ICLR 2023] One Transformer Can Understand Both 2D & 3D Molecular Data (official implementation)
  ☆215Updated 2 years ago
• hwwang55 / MolR
  Chemical-Reaction-Aware Molecule Representation Learning
  ☆80Updated 3 years ago
• THUDM / MSAGPT
  MSAGPT
  ☆35Updated 10 months ago