AlphaFold2.ipynb LICENSE Readme data_preprocessing.py datasets.zip encodes.py trained_models.zip Breadcrumbs ARTNet / AlphaFold2.ipynb Latest commit Cannot retrieve latest commit at this time. HistoryHistory File metadata and controls Preview Code Blame 680 lines (680 loc) · 37.9 KB Raw Viewer...
29 changes: 20 additions & 9 deletions 29 notebooks/AlphaFold.ipynb Original file line numberDiff line numberDiff line change @@ -14,7 +14,7 @@ "\n", "In comparison to AlphaFold v2.1.0, this Colab notebook uses **no templates (homologous structures)** and a selected portion of ...
AlphaFold2.ipynb - Colaboratory (google.com) ColabFold v1.5.2-patch: AlphaFold2 using MMseqs2,这个可能更轻量化。运行成功了。 值得注意的是,选取预测的结果时,看文件名的rank值,rank0最可信。而不是根据model数,以前我用的都是model5。 随后又从github issues 区找了一个jackhmmer fail的话题,copy了解...
在Google Colab 上使用 RF Diffusion(未指定 Hotspot) 如何使用 RF Diffusion 可以参考这个链接:https://colab.research.google.com/github/sokrypton/ColabDesign/blob/v1.1.1/rf/examples/diffusion.ipynb。你只需在Google Colab中打开相应的笔记本,然后点击运行按钮即可。 以下操作使用了蛋白质结构6M0J作为示例。结...
AlphaFold的正式运算需要的资源非常庞大,个人或者小团队如果家里没矿的话,想自己搭平台运算基本没戏;好在谷歌提供了一个免费的云端平台Colab(https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb),可以运行精简版的AlphaFold。平台入口就在AlphaFold数据库的底端FAQ里。
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb 便打开了这个工作流程(ipynb)。首先填写想要折叠的蛋白质序列,如果您在测试它的精准性,可以从PBD网站下载fasta文件,把序列粘贴到sequence这一行。MSA_models选择建议MMseqs,num_model建议选5,用五个模型进行折叠,Alphafold折叠...
内坐标详细可以参考:https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/3_Kinematics/3_0_FoldTree.ipynb 模拟退火算法: 用于构象优化阶段,参见wiki Fragment Assembly机制-关键组件 参考: Macromolecular Modeling with Rosetta The coming of age of de novo protein design ...
AlphaFold的正式运算需要的资源非常庞大,个人或者小团队如果家里没矿的话,想自己搭平台运算基本没戏;好在谷歌提供了一个免费的云端平台Colab(https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb),可以运行精简版的AlphaFold。平台入口就在AlphaFold数据库的底端FAQ里。
https://github.com/jurgjn/af2_pockets. Protein complexes:https://gitlab.com/ElofssonLab/FoldDock,https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb. Model building:https://github.com/tristanic/pae_to_domains. ...
#添加设置文件 settings_path = os.path.join(output_dir,"settings.txt") with open(settings_path, "w") as text_file: text_file.write(f"notebook=https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb\n") text_file.write(f"sequence={ori_sequen...