Integrated Platform for Assessing the Quality of Macromolecular Models

TL;DR

This paper introduces a new platform for quickly evaluating and comparing the quality of macromolecular models used in biomedical research.

Contribution

The novel contribution is an integrated system combining multiple databases for structural analysis within PyMOL.

Findings

The platform integrates resources like RCSB PDB, PDBe, and AlphaFold DB for model evaluation.

It provides a streamlined workflow for comparing cryoEM and crystallography-derived protein models.

The system is implemented in PyMOL 3.1 for efficient structural analysis.

Abstract

Macromolecular models are crucial for biomedical research, particularly in drug discovery. However, variations in model quality can impact the reliability of downstream analyses [1, 2]. To advance the evaluation of macromolecular structures, we developed an integrated system for the rapid exploration and comparison of protein structure models derived from cryoEM and crystallography experiments. Our platform seamlessly incorporates multiple resources, including RCSB PDB [3], PDBe [4], PDBj [5], UniProt [6], PDB-REDO [7, 8], EMDB [9], and AlphaFold DB [10]. Currently, the system operates within the PyMOL 3.1 ecosystem, providing an efficient and streamlined workflow for structural analysis.