ArticleFrontiers in molecular biosciences2025
Reformulation of the protein databank for real-time search of geometrical attributes of protein structures.
Article in Frontiers in molecular biosciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Introduction: In this study, we introduce the design and implementation of PDBMine, a large-scale, queryable platform for mining sequence-structure statistics from the Protein Data Bank (PDB). PDBMine enables rapid analysis of local conformational trends across proteins by extracting dihedral angles and sequence patterns at scale. In addition to the design and implementation of PDBMine, we also present results validating its ability to return structurally meaningful information. Methods: We first assess the accuracy of its dihedral angle distributions by comparing them to established Ramachandran space and verifying expected behaviors of residues such as glycine and proline. We then use PDBMine to analyze the statistical properties of amino acid subsequences of length Results: Our findings reveal that longer Discussion: These results highlight PDBMine's potential as a versatile tool for structure validation, statistical modeling, and probing the principles that govern sequence-structure compatibility in proteins.
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