PDB Manipulation Suite (PDBMS): A browser-based toolkit for PDB file manipulation, molecule building and biophysical analysis, easily extendable via reasoning models

We present here the PDB Manipulation Suite (PDBMS), a modular hub of web apps and platforms designed for the seamless creation, edition, and analysis of biomolecular coordinate files.The PDBMS is written entirely for client-side execution in web browsers, providing a "zero-footprint" environment available out of the box at https://pdbms.altervista.org/with zero installs, no downloads, and no registration.This architecture ensures that all calculations occur locally, meaning that sensitive data never leaves the user's machine-critical for proprietary structural data-while maintaining the responsiveness of a local application.The suite is organized into specialized sub-platforms: PDBMS-tools for rapid structure editing, renumbering, format conversion and data mapping; Web-PackMol for the assembly of complex molecular systems;Web-MDA and the Conformational Ensemble Inspector for the deep analysis and inspection of molecular dynamics trajectories, BioEmu predictions, docking poses, and other kinds of ensembles.Example functionalities include a variety of analyses to infer structural details, dynamics and interactions across molecules and time or ensemble indexes, to aid in the visualization of various kinds of data including AlphaFold 3 confidence scores and outputs from modern NMR spectroscopy pipelines.Since the source code is inherently open and was developed largely with AI reasoning models at Google's AI Studio, it is extremely easy to modify or add new functionalities at will.We demonstrate this by providing tools to assist the editing and visualization of outputs from modern software like NMRtist and Sparky; and also demonstrate how an AI agent built into the Web-MDA app can provide new functionalities on request.We hope PDBMS will provide an environment for structural bioinformaticians and molecular modelers to perform complex tasks while maintaining absolute data confidentiality, extreme portability across devices and operating systems, and maximal flexibility.