PDB-Explorer

PDB-Explorer maps and analyzes the structural diversity of biological macromolecules in the RCSB Protein Data Bank using a 136-dimensional atom pair 3D-fingerprint (3DP) that encodes through-space atom-pair distributions to represent molecular shape.

Key Features:

• 3D-Shape Fingerprinting (3DP): A 136-dimensional atom pair 3D-fingerprint (3DP) categorizes atom pairs at varying through-space distances to encode molecular shape for proteins, peptides, and nucleic acids.
• 3DP-space visualization: A color-coded map represents chemical space in 3DP-space where map pixels correspond to one or more PDB entries and structures are rendered as ribbon diagrams.
• Nearest-neighbor searches: Retrieval using the 3DP similarity metric identifies structurally related biomolecules from small peptides to large multiprotein complexes with results comparable to traditional 3D-alignment algorithms.
• Principal Component Analysis (PCA): PCA is applied to 3DP vectors to project and visualize PDB entries and to group structures by shape similarity.
• Superfamily clustering: Automatic clustering groups proteins from the same superfamilies into tight clusters based on 3DP similarity to reveal evolutionary and functional relationships.

Scientific Applications:

• Exploration of structural diversity: Mapping PDB entries in 3DP-space enables systematic exploration of structural variation and similarity among biological macromolecules.
• Identification of related structures: 3DP-based similarity searches facilitate detection of structurally related proteins and complexes for comparative and functional analyses.
• Visualization of molecular shapes: 3DP projections and ribbon representations support analysis of molecular shape relevant to folding, stability, and intermolecular interactions.
• Hypothesis generation: Rapid comparison of structures in 3DP-space aids generation of hypotheses about structure–function and evolutionary relationships.

Methodology:

Computation of a 136-dimensional atom pair 3D-fingerprint (3DP) by binning atom-pair distances; projection of 3DP vectors using PCA; nearest-neighbor retrieval using the 3DP similarity metric; clustering of entries by 3DP similarity.