预测突变对蛋白蛋白之间相互作用影响学习笔记

1. Cartesian_ddG: 更快更准确的单点突变自由能预测方法

参考1:https://zhuanlan.zhihu.com/p/65451836
参考2:https://docs.rosettacommons.org/docs/latest/cartesian-ddG
参考3:https://docs.rosettacommons.org/docs/latest/application_documentation/analysis/ddg-monomer

Rosetta安装方法见此篇文章:http://billvm.com/archives/shi-yong-dockerjin-xing-rosettaan-zhuang-bi-ji

#设置mpirun可以root运行
export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1

1. 优化蛋白-蛋白复合物的结构，使用relax方法

# relax
relax.mpi.macosclangrelease -s $file.pdb \
    -relax:constrain_relax_to_start_coords \
    -ramp_constraints false \
    -relax:coord_constrain_sidechains \
    -nstruct 40 \
    -ex1 \
    -ex2 \
    -use_input_sc \
    -flip_HNQ \
    -no_optH false

# 多线程
mpirun -n 12 relax.mpi.macosclangrelease -s $file.pdb \
    -relax:constrain_relax_to_start_coords \
    -ramp_constraints false \
    -relax:coord_constrain_sidechains \
    -nstruct 40 \
    -ex1 \
    -ex2 \
    -use_input_sc \
    -flip_HNQ \
    -no_optH false

2. 准备mutfile文件

注意！此处的89为pose序号，而非PDB中的残基号，设置错误一定会报错。（跑的时候不要带注释，新版本的app中，不能有中文和注释）

total 3 #this is the total number of mutations being made.
2 # the number of mutations made
G 1 A # the wild-type aa, the residue number, and the mutant aa
W 6 Y # the wild-type aa, the residue number, and the mutant aa
1 #the number of mutations
F 10 Y # the wild-type aa, the residue number, and the mutant aa