mutation/README.md

progress

• [*] def 函数1（输入蛋白pdb和突变list，输出突变后的pdb）：{调用EvoEF2突变}
• [*] def 函数2（输入蛋白pdb和突变list，输出突变后的pdb）：{调用Scwrl4突变}
• [*] def 函数3（输入蛋白pdb和突变list，输出突变后的pdb）：{调用foldx突变}
• [*] def 函数4（输入蛋白pdb和突变list，输出突变后的pdb）：{调用rosetta突变}
• def 函数5（输入蛋白pdb和突变list，输出突变后的pdb）：{调用opus-mut突变}
• [*] def 函数5（输入蛋白pdb和突变list，输出突变后的pdb）：{调用pymol突变}

install

apt update && apt install curl wget git -y

conda create -n mutation python=3.10 -y
conda install -c conda-forge biopython pyrosetta loguru click pymol-open-source -y # 安装日志库 # ! pyrosetta 很大需要配置私有源

docker

docker pull ubuntu:22.04

mutation.py test

evoEF2 test

install

unzip EvoEF2-master.zip
cd EvoEF2-master
./build.sh

python mutation.py evoef2 -p 4i24.pdb -m test.list

foldX test

python mutation.py foldx -p 4i24.pdb -m test.list

rosetta test

python mutation.py rosetta -p 4i24.pdb -m test.list

scwrl4 test

install : chmod +x install_scwrl4.0.2_64bit_2020_linux

python mutation.py scwrl4 -p 4i24.pdb -m test.list

opus-mut test

1. Use mk_mut_backbone.py to generate original WT backbone file and mutants backbones. In this step, you need to set the original PDB file path in line 97 native_filepath = ./3phv.pdb. Then set the mutations you want in line 108 mutations = ["P9Y", "V82I", "V82G", "I84N", "L90R"]. Here, we use hiv.pdb and mutation Q2E as an example.

2. List the backbone paths in bb_list. ls *bb > bb_list

3. Use run_opus_mut.py to generate the results of OPUS-Mut (.mut). In this step, you need to activate the environment created by mut.yml file. Also, a GPU device is required and should be set in line 13 os.environ["CUDA_VISIBLE_DEVICES"] = "0". cuda10.1 is also required.

4. Use get_difference_summation.py to calculate the differences between WT and mutants (.changes). In this step, you need to set the original PDB file name in line 20 ori_name = "3phv", and line 115 if filename == "3phv": continue. Note that, the code line 130 if not int(resid) in [25, 26, 27]: continue can be used to calculate the differences from specific residues (Sdiff_critical). When calculating the differences from all residues (Sdiff), you need to comment this line, and also uncomment the line between 134-143 to avoid the influence of outliers. .

根据opus-mut的软件使用教程来看，opus仅支持单链进行突变，也就是说如果需要对多链进行突变，需要对多链单链分割，然后对分割后的多链进行突变，然后再将突变后的单链进行合并。

注意opus-mut需要从github仓库获取

pymol test

python mutation.py pymol -p 4i24.pdb -c B -r 797 -t GLY

统一接口调用

完成 2023-08-22

调用方法统一为 test.list文件（方便多位点突变）

完成 2023-08-25

封装环境至docker镜像

使用scwrl4进行残基序列突变

测试：

python mutation.py scwrl4 -p 4i24.pdb -m test.list

construct docker images

docker cp /home/share_data/opus_mut.zip a97ed867a713:/work

Docker 镜像使用

rm ../dockertest/* -rf && cp ../4i24.pdb ../dockertest && cp ../test.list ../dockertest
docker run --rm -it -v /home/zenglingyu/tools/dockertest:/work hotwa/mutation:latest <software> -p /work/4i24.pdb -m /work/test.list
# example
docker run --rm -it -v /home/zenglingyu/tools/dockertest:/work hotwa/test2:latest rosetta -p /work/4i24.pdb -m /work/test.list
docker run --rm -it -v /home/zenglingyu/tools/dockertest:/work hotwa/test2:latest scwrl4 -p /work/4i24.pdb -m /work/test.list
docker run --rm -it -v /home/zenglingyu/tools/dockertest:/work hotwa/test2:latest evoef2 -p /work/4i24.pdb -m /work/test.list

非root测试

docker run --rm -it -v /home/zenglingyu/tools/dockertest:/home/developer/work hotwa/test1:latest rosetta -p /home/developer/work/4i24.pdb -m /home/developer/work/test.list

构建docker镜像

缺少pyrosetta-2023.31+release.1799523-py311_0.tar.bz2文件，需要从官网下载手动安装，太大了。上传太慢

相关资源文件： 资源盘

网盘 链接：https://pan.baidu.com/s/1auuSM4rcQUC_gcYBwyRSXA?pwd=vfcu 提取码：vfcu

突变文件介绍

突变文件格式 文件名: individual_list.txt

内容结构:

每个突变写在一行上，以“;”结束。 一个突变中的多个单点突变用“,”分隔。 突变表示:

第一个字母是参考氨基酸（原氨基酸）。 第二个字母是氨基酸所在的链标识符。 紧跟着的数字是氨基酸在链中的位置。 最后一个字母是突变后的氨基酸。 示例:

CA171A,DB180E;

第一个突变：链A上位置171的C（半胱氨酸）突变为A（丙氨酸）。 第二个突变：链B上位置180的D（天冬氨酸）突变为E（谷氨酸）。 注意:

不应有空格或其他多余字符。 这种格式允许用户明确指定在蛋白质复合体中哪些氨基酸应进行突变，从而提供高度定制的突变模型。

docker build

docker build --progress=plain -t hotwa/mutation:latest -f developer.Dockerfile .

test

docker run --rm --entrypoint /bin/bash --user=1000:1000 -it -v ./test:/home/developer/work hotwa/mutation:latest 

Docker 镜像使用

docker run --rm -it -v /home/zenglingyu/tools/dockertest:/work hotwa/mutation:latest <software> -p /work/4i24.pdb -m /work/individual_list.txt
# example
docker run --rm -it -v ./test:/home/developer/work hotwa/mutation:latest rosetta -p /home/developer/work/4i24.pdb -m /home/developer/work/individual_list.txt
docker run --rm -it -v ./test:/home/developer/work hotwa/mutation:latest scwrl4 -p /home/developer/work/4i24.pdb -m /home/developer/work/individual_list.txt
docker run --rm -it -v ./test:/home/developer/work hotwa/mutation:latest evoef2 -p /home/developer/work/4i24.pdb -m /home/developer/work/individual_list.txt
docker run --rm -it -v ./test:/home/developer/work hotwa/mutation:latest pymol -p /home/developer/work/4i24.pdb -m /home/developer/work/individual_list.txt
docker run --rm -it -v ./test:/home/developer/work hotwa/mutation:latest foldx -p /home/developer/work/4i24.pdb -m /home/developer/work/individual_list.txt

2023-9-20 2023-9-21

--no-fix 不修复

突变残基周围也不修复

pymol版本优先提供

flodx: 默认删除ATOM其他结构（强制删除），会自动修复（可关闭）

pymol仅突变，修复突变残基周围的构象

scwrl4: 只能预测侧链，会改变蛋白构象

pyrosetta: 会尝试自动修复，不断报错，直到程序终止

evoef2: 报错pdb格式无法修复

 ############################################################################################
                                    EvoEF2                                                  
  A framework for macromolecular modeling, e.g.,protein design, protein side-chain packing, 
protein structure energy minimization, add and optimize hydrogen bonds, build mutant model, 
calculate protein folding stability, calculate protein-protein binding free energy, etc     


  Copyright (c) Xiaoqiang Huang (xiaoqiah@umich.edu; tommyhuangthu@foxmail.com)
  Dept. of Computational Medicine & Bioinformatics
  Medical School
  University of Michigan
############################################################################################
command BuildMutant works
coordinate of atom H on residue A ASN 70 is invalid, please check
ValueError: in file src/Residue.cpp function ResidueCalcAllAtomXYZ() line 729, not all atoms' XYZ can be calculated for residue ASN in chain A 70
ValueError: in file src/Chain.cpp function ChainCalcAllAtomXYZ() line 208

2023-09-21 14:42:43.468 | ERROR    | __main__:evoEF2base:163 - 1jpz_mcpbpy_Model_0001.pdb mutation failed! mutation line: CA62G,FA87V,AA74Q,SA72G;
2023-09-21 14:42:43.469 | INFO     | __main__:execute_evoef2:496 - EvoEF2 mutation 1jpz_mcpbpy.pdb finished

2024-09-16

foldx 突变有问题

压缩打包

zip -r Aps_Models.zip Aps_Model_*.pdb
tar -czf Aps_Models.tar.gz Aps_Model_*.pdb