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Codes_for_FoldX

Scripts

some useful codes for foldx

pdb2seq

convert a pdb file to a fasta
usage: python pdb2seq.py name.pdb

prepare4scan

to build the config file for foldx to preform a saturated mutation scan
usage: python prepare4scan.py -i seq.fasta -p name_Repair.pdb

prepare4buildmodel

prepare the individual list for BuildModel in FoldX
usage:python prepare4buildmodel.py -i PS_pdbid_scanning_output.txt -l a_number

multiple_threads_positionscan

To run the positionscan in a faster way with more threads
usage:python multiple_threads_foldx_positioncsan.py -s pdb -nt number_of_threads

GUI script

For Biologists who has difficulty in command-line tools.
This script can be simply builded by: pyinstaller GUI.py

Guide for the most people

  1. Download the GUI.py
  2. make sure you have tkinter installed, which can be install by the following command:
  1. run python3 GUI.py
  2. Usage
  • After the PDB ID, you can enter the four-digit PDB code, or you can enter six digits: 3wzl_A represents the A chain of 3wzl, and the acquisition is directly downloaded from the RCSB database.
  • At present, the PDB ID and the input PDB are synchronized and can be modified by user. Foldx Repair is a preparation step for calculating the mutation ddG, and the calculation of A chain of 3wzl takes about several minutes.
  • Mutation currently only supports single point mutations (eg. M1A, mutate the first Met to Ala)
  • The <"Foldx Position Scan"> is currently not recommended. This is a saturated mutation scanner, the input is the number of threads, because foldx does not support MPI, so this is a manual multi-thread. See multiple_threads_positionscan for details. If you have any questions, please contact

GUI版本foldx使用教程（目前支持MAC,LINUX)

因为foldx本身是需要许可证的，所以我不能在这里提供下载，以下的说明是针对我所在的组里面的成员的。

1.安装

  • 打开终端
  • 输入： mkdir EasyFoldx
  • 将压缩包中的foldx和rotabase.txt拷贝入EasyFoldx
  • 在dist文件夹内双击part_manger
  1. 使用
  • PDB ID 后可输入四位PDB code，也可以输入六位：3wzl_A即代表3wzl的A链，fetch是从RCSB数据库直接下载。
  • 目前PDB ID和Input PDB是同步的，可自行修改，Foldx Repair是计算突变ddG的准备步骤，3wzl的A链大概需要几分钟。
  • Mutation目前仅支持单点突变，（如M1A，即为第一位的Met突变为Ala）
  • Number of Threads目前不建议使用，这是一个饱和突变扫描程序，输入为线程数，因为foldx不支持MPI，所以这是一个手动多线程。具体内容可参见multiple_threads_positionscan。
    如有任何问题，请联系

GUI version foldx tutorial (currently supports MAC and LINUX only)

Beacues Foldx requires lisence, I can't provide it here, the following guide is for members in the lab I'm working with.

  1. Installation
  • Open terminal
  • Enter: mkdir EasyFoldx
  • Copy foldx and rotabase.txt from the archive to EasyFoldx
  • Double-click part_manger in the dist folder
  1. Usage
  • After the PDB ID, you can enter the four-digit PDB code, or you can enter six digits: 3wzl_A represents the A chain of 3wzl, and the acquisition is directly downloaded from the RCSB database.
  • At present, the PDB ID and the input PDB are synchronized and can be modified by user. Foldx Repair is a preparation step for calculating the mutation ddG, and the calculation of A chain of 3wzl takes about several minutes.
  • Mutation currently only supports single point mutations (eg. M1A, mutate the first Met to Ala)
  • The <"Foldx Position Scan"> is currently not recommended. This is a saturated mutation scanner, the input is the number of threads, because foldx does not support MPI, so this is a manual multi-thread. See multiple_threads_positionscan for details.
    If you have any questions, please contact

PS:

The FoldX5 provides a graphical user interface available as a python plugin for the YASARA molecular viewer.

Reference

  1. Javier Delgado, Leandro G Radusky, Damiano Cianferoni, Luis Serrano, FoldX 5.0: working with RNA, small molecules and a new graphical interface, Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4168–4169, https://doi.org/10.1093/bioinformatics/btz184