GAX: Genetic Algorithm for minimum ensemble fitting of SAXS data
Yasaman Karami, Michaël Nilges, Guillaume · Zenodo (CERN European Organization for Nuclear Research) · 2022
This repository contains all the data we used for evaluating GAX; a method based on genetic algorithm for extracting a minimum ensemble of conformations from the pool of conformations generated by molecular dynamics simulations that fit SAXS data. The case studies are: i) the protein PTPN4 with two domains (PDZ and PTP), ii) the tandem WW domains of the formin-binding protein 21 (FBP21-WWs), iii) the AC-CaM complex formed between the catalytic domain (AC) of adenylate cyclase toxin and calmodulin (CaM), iv) the K63-linked diubiquitin (K63-Ub$_2$) consisting of two subunits (distal and proximal ubiquitin). All the SAXS data and back-calculated profiles from MD simulations are deposited here. Also the trajectories generated for the PTPN4, FBP21-WWs, and AC-CaM are deposited. The simulations were carried out using GROMACS 2020.4 package.