Alternatives and similar repositories for ptm-mamba

Users that are interested in ptm-mamba are comparing it to the libraries listed below

• duolinwang / S-PLM
  S-PLM: Structure-aware Protein Language Model via Contrastive Learning between Sequence and Structure
  ☆67Updated 3 weeks ago
• TencentAI4S / tfold
  open source code for Tencent tFold
  ☆104Updated 4 months ago
• hugohrban / ProGen2-finetuning
  Finetuning ProGen2 protein language model for generation of protein sequences from selected protein families.
  ☆62Updated 5 months ago
• OATML-Markslab / ProteinNPT
  Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"
  ☆114Updated 4 months ago
• moritzgls / ESM-Effect
  ☆15Updated 5 months ago
• uci-cbcl / esm-efficient
  Efficient implementatin of ESM family.
  ☆58Updated 5 months ago
• ml4bio / RiboDiffusion
  ISMB-24/Bioinformatics: Tertiary Structure-based RNA Inverse Folding with Generative Diffusion Models
  ☆49Updated 8 months ago
• evo-design / protein-dpo
  Aligning protein generative models with experimental fitness
  ☆99Updated 2 months ago
• Eikor / InstructPLM
  The first large protein language model trained follows structure instructions.
  ☆82Updated last month
• ai4protein / ProSST
  🧬 Advanced hybrid language model for directed protein evolution. (NeurIPS 2024)
  ☆129Updated last month
• ai4protein / ProtSSN
  🧬 Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2…
  ☆69Updated 2 months ago
• varun-shanker / structural-evolution
  ☆109Updated last year
• zhengkangjie / ESM-AA
  ☆73Updated 5 months ago
• DeepGraphLearning / S3F
  Sequence-Structure-Surface Model for Protein Fitness Prediction (S3F)
  ☆40Updated 7 months ago
• jiaqingxie / DeepProtein
  Deep Learning Library and Benchmark for Protein Sequence Learning (Bioinformatics 2025)
  ☆30Updated 2 weeks ago
• EDAPINENUT / GeoAB
  This is the official repository of paper - GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation (ICML2024)
  ☆40Updated last year
• THUNLP-MT / dyMEAN
  This repo contains the codes for our paper "End-to-End Full-Atom Antibody Design"
  ☆113Updated 4 months ago
• pengzhangzhi / ab_opt
  Official implementation of Generative Diffusion Models for Antibody Design, Docking, and Optimization.
  ☆60Updated last year
• WillHua127 / EnzymeFlow
  Official repository of EnzymeFlow
  ☆91Updated 7 months ago
• westlake-repl / SaprotHub
  Making Protein Modeling Accessible to All Biologists
  ☆114Updated this week
• RSchmirler / data-repo_plm-finetune-eval
  Data repository for "Fine-tuning protein language models boosts predictions across diverse tasks"
  ☆42Updated 10 months ago
• TencentAI4S / IgGM
  [ICLR2025] Official Implementation of IgGM: A Generative Model for Functional Antibody and Nanobody Design
  ☆73Updated 2 months ago
• Graylab / FLAb
  Fitness landscapes for antibodies
  ☆72Updated 6 months ago
• DeepGraphLearning / GearBind
  Pretrainable geometric graph neural network for antibody affinity maturation
  ☆59Updated 3 months ago
• Exscientia / abodybuilder3
  ☆58Updated 8 months ago
• instadeepai / protein-structure-tokenizer
  Official implementation of "Learning the language of protein structures"
  ☆36Updated 3 weeks ago
• shuaizengMU / PEFT-SP
  ☆18Updated 8 months ago
• zhanghaicang / carbonmatrix_public
  ☆115Updated last month
• WillHua127 / ReactZyme
  Official repository of ReactZyme
  ☆34Updated 9 months ago
• chao1224 / ProteinDT
  A Text-guided Protein Design Framework, Nat Mach Intell 2025 (https://www.nature.com/articles/s42256-025-01011-z)
  ☆90Updated 6 months ago