PDBeMotif

PDBeMotif enables exploration of conserved sequence motifs, 3D structural motifs, and ligand interactions within Protein Data Bank (PDB) entries to support analysis of protein structure–function relationships.

Key Features:

• Motif Identification: Identifies sequence-based motifs and 3D structural motifs in the context of ligand interactions and binding sites.
• Advanced Search Capabilities: Implements algorithms for comprehensive searches across motif types including chemical fragments, phi/psi sequences, super-secondary structures, and small 3D structural motifs within the PDB.
• Visualization and Alignment Tools: Provides sequence and 3D multiple alignment capabilities to compare motif instances and structural contexts.
• Integrated Analysis (MSDmotif): Integrated with MSDmotif to produce and aggregate motif statistics for downstream analysis.
• Motif Statistics: Computes molecule and motif binding statistics, amino acid occurrence within motifs, and correlations of side-chain charges.
• Statistical Insights: Generates Ramachandran plots per residue to report conformational distributions associated with motif occurrences.
• Ligand Fragment Library: Associates binding statistics with a ligand fragment library to enable analysis of chemical fragment–motif interactions.
• Data Access: Serves data via the Distributed Annotation System (DAS) protocol and supports XML requests and responses.

Scientific Applications:

• 3D Structure Prediction: Supports identification of recurrent structural motifs used in comparative and predictive modelling of protein folds.
• Protein Modeling: Provides motif occurrences and alignments to inform homology modelling and structural refinement.
• Drug Design and Ligand Interaction Analysis: Enables analysis of motif–ligand interactions and fragment binding statistics to guide small-molecule design and optimization.
• Molecular Mechanism Elucidation: Facilitates analysis of residue-level conformational preferences and side-chain charge correlations to understand functional mechanisms.

Methodology:

Performs motif searches across the PDB using algorithms for chemical fragment, phi/psi sequence, super-secondary structure, and small 3D motif matching; computes sequence and 3D multiple alignments and motif statistics including Ramachandran plots; links motif binding statistics to a ligand fragment library and exposes results via DAS and XML.