Input structures and EvoMut analysis results for oxidation stability case studies

This repository contains the structural inputs and EvoMut analysis resultsassociated with the manuscript: "EvoMut: A Computational Framework for Engineering Oxidative Stability in Proteins" Each case study described in the manuscript is organized in a separate folder(A1AT, AmyA, AmyC, VP). For each protein the folder holds the input files usedfor the analysis, together with an evomut_results/ subfolder containing thegenerated output. INPUT FILES (located directly inside each protein folder) - PDB structure file (<pdbid>.pdb) The three-dimensional structure used for the analysis. - HSSP alignment file (<pdbid>.hssp) The multiple-sequence alignment used for evolutionary profiling. - analysis_config.txt A plain-text record of every parameter used for the run, so that the results can be reproduced. It is organized in two steps: Step 1 - Input data: Protein name, PDB file, HSSP file, analyzed chain, the reference sequence (auto-detected from the structure or provided manually), and optional functional-site annotations. Step 2 - Oxidation Stability Parameters: The complete oxidation-risk scoring configuration, including: * Oxidant species and combine mode - the reactive species the run was scored against. Selecting all six species under the unknown-oxidant aggregate reproduces the screening default. * RSA (relative solvent accessibility) threshold. * Distance metric and neighbor cutoff (Calpha-Calpha, in Angstrom). * ORI term weights: wE (exposure), wC (chemistry), wS (site context), wK (conservation). * Per-residue chemical susceptibility weights: Met, Cys (free), Cys (disulfide-bonded), Trp, Tyr, His, Lys, Arg. The UniProt identifier is normally retrieved automatically from the information stored in the PDB structure and is used to obtain the reference protein sequence. In cases where the UniProt identifier cannot be determined automatically, the reference sequence can be provided manually and specified in analysis_config.txt. For multi-chain protein structures, EvoMut automatically identifies residues that form inter-chain contacts and incorporates these positions as functionally relevant binding residues during the analysis. For single-chain structures, users may optionally specify functional-site residues (for example catalytic residues in enzymes) in analysis_config.txt to provide additional functional context. OUTPUT FILES evomut_results/ Contains the output generated by EvoMut: oxidation risk index (ORI) tables and mutation feasibility results for the analyzed residues, provided as Excel workbooks named <Protein>_<Residue>_ORI.xlsx (for example AmyA_M349_ORI.xlsx). The EvoMut web server used for the analyses is freely available at:https://proteus.cmm.uga.edu/evomut