Supplementary Simulation Data for "Computational and experimental assessment of key interdomain residues controlling the fold-switch of RfaH"

Additional simulation data for "Computational and experimental assessment of key interdomain residues controlling the fold-switch of RfaH" Content: 'AA-SBM': Contains a total of 4 folders, which require the use of SMOG2 and the GROMACS v4.5.4 version with added Gaussian contact potentials available at the SMOG server (https://smog-server.org). 'pdb': Includes the SMOG2-ready PDB file of full-length RfaH generated using MODELLER, based on PDBs 2OUG and 5OND, and further minimized in explicit solvent using GROMACS v4.5.3 and the Amber ff99SB-ILDN force field. 'smog': Contains the SMOG2-generated files for MD simulations using All-Atom Structure-Based Models (SBMs). 'simulate': Includes simple scripts for running simulations at several temperatures on an HPC cluster 'analysis': Contains simple scripts for concatenation of energies and trajectories, extraction of the potential energy of the system and the number of native contacts (Q) for each simulation run, and a script for running the weighted histogram analysis method based on the java WHAM.jar available with SMOG2. 'ColabFold': Contains a total of 2 folders with results from protein structure predictions using ColabFold v1.5.5 (https://colabfold.com). 'structures': Contains 8 .tar.gz files with the predicted structures of several E. coli RfaH variants (WT, E48A, F126A, I129A, E136A, R138A, S139A, L142A, L143A, I146A, N147A, V154) under different conditions. Each folder within the .tar.gz file contains a total of 600 predicted structures for all variants (50 predicted structures per variant), as well as the results of analyzing these structures based on RMSD using k-means clustering and based on TM-score using hierarchical clustering. r3_s10_nodrop: 5 model parameters, 3 recycles, 10 seeds, no dropouts r3_s10_nodrop_MSA: 5 model parameters, 3 recycles, 10 seeds, no dropouts, using the same MSA as RfaH WT for all RfaH variants r3_s10_drop: 5 model parameters, 3 recycles, 10 seeds, with dropouts r3_s10_drop_MSA: 5 model parameters, 3 recycles, 10 seeds, with dropouts, using the same MSA as RfaH WT for all RfaH variants r12_s10_nodrop: 5 model parameters, 12 recycles, 10 seeds, no dropouts r12_s10_nodrop_MSA: 5 model parameters, 12 recycles, 10 seeds, no dropouts, using the same MSA as RfaH WT for all RfaH variants r12_s10_drop: 5 model parameters, 12 recycles, 10 seeds, with dropouts r12_s10_drop_MSA: 5 model parameters, 12 recycles, 10 seeds, with dropouts, using the same MSA as RfaH WT for all RfaH variants 'analysis': Contains 2 Jupyter Notebooks for usage in Google Colab to perform k-means clustering analysis of the structures obtained by ColabFold based on the RMSD of residues 126-131 Hierarchical clustering analysis of the structures obtained by ColabFold based on the TM-score against the best predicted structure (rank 1) for each variant.