mpnn_utils.py resave.py run_protein_mpnn.py testing.ipynb setup .gitignore README.md Breadcrumbs proteinmpnn /run / generate_json.py Latest commit Cannot retrieve latest commit at this time. HistoryHistory Breadcrumbs proteinmpnn /run / generate_json.pyTop File metadata and controls Code Blame...
Pytorch implementation for ICML 2024 paper Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency. - Proteus/ProteinMPNN/protein_mpnn_run.py at master · Wangchentong/Proteus
ProteinMPNN中的parse_cif_noX.py文件主要是用于从生物大分子结构CIF文件中数据清洗提取信息并用于后续的模型输入数据。这里对该脚本进行学习记录以便后续查找。如下图所示,该脚本的输入是从RCSB数据库中下载的.cif.gz文件,该脚本对CIF文件进行解析生成了两个字典变量chains和metadata。chains里面含有每条链的序列,原子坐...
make_bias_per_res_dict.pymake_pos_neg_tied_positions_dict.pymake_pssm_input_dict.pymake_omit_AA.pymake_pssm_dict.py 7. training 为了训练/重新训练ProteinMPNN,克隆这个github repo并安装Python =3.0,PyTorch,Numpy。 多链训练数据(16.5 GB,PDB biounits,208月21日)可以从这里下载:files.ipd.uw.ed...
H. et al. Improving protein expression, stability, and function with proteinmpnn. J. Am. Chem. Soc. 146, 2054–2061 (2024). Article CAS PubMed PubMed Central MATH Google Scholar Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using diamond. Nat. ...
PyMOL58along various angles of approach, such that the peptide binds to opposite sides of the fusion construct. We used RFDiffusion33to build a short loop region connecting both hinges into a single chain. ProteinMPNN27was used to redesign the interface between these two hinge domains, without...
Robust deep learning–based protein sequence design using ProteinMPNN 2022, Science RETHINKING ATTENTION WITH PERFORMERS 2021, ICLR 2021 - 9th International Conference on Learning Representations Role of nanoscale antigen organization on B-cell activation probed using DNA origami 2020, Nature Nanotechnology ...
PyMOL58along various angles of approach, such that the peptide binds to opposite sides of the fusion construct. We used RFDiffusion33to build a short loop region connecting both hinges into a single chain. ProteinMPNN27was used to redesign the interface between these two hinge domains, without...
our in-house version of ProteinMPNN. Contribute to Kuhlman-Lab/proteinmpnn development by creating an account on GitHub.
our in-house version of ProteinMPNN. Contribute to Kuhlman-Lab/proteinmpnn development by creating an account on GitHub.