Web Platform for Automated RMSD Calculation Across Heterogeneous Molecular Files

The Root Mean Square Deviation (RMSD) is essential for molecular conformational comparison in computational chemistry and structural bioinformatics, with a wide range of uses from protein-ligand docking pose comparison to analysis of molecular dynamics trajectories. One challenge in computing RMSD is ensuring a precise matching of atoms between structures, especially with different file formats like PDB, PDBQT, SDF, MOL2, and XYZ, each with their own conventions for atom ordering, naming, and content. To ensure consistency in atom mapping, scientists often dedicate a significant amount of time to manually preprocess files, a process that is both cumbersome and error-prone, ultimately discouraging reproducibility. In response to this bottleneck, we have developed a web platform that automates the computation of RMSD for molecules across different file formats. The platform utilizes a strong backend pipeline to standardize variable inputs into a common molecular representation, resulting in a consistent atom map. This removes the necessity for manual intervention and enables accurate and direct RMSD computation. The program utilizes the Streamlit framework for a user-friendly interface and is hosted on an institutional server for widespread use. Preliminary findings show that the platform can accurately compute RMSD values between files of varying formats, simplifying a crucial step in molecular modeling. This advancement marks a significant achievement in enhancing the efficiency, accessibility, and reproducibility of structural comparisons in computational life sciences.