ProteinsPlus

ProteinsPlus provides a unified interface to computational tools for structure-based molecular modeling, leveraging over 126,000 Protein Data Bank (PDB) structures to support tasks in drug discovery, crop science, and biotechnology.

Key Features:

• Structure Quality Assessment: Utilizes EDIA to evaluate protein structure quality for downstream analysis.
• Hydrogen Placement: Uses Protoss to place hydrogen atoms in protein structures.
• Alternative Conformation Search: Employs SIENA to identify alternative conformations within protein structures.
• 2D Interaction Diagrams: Generates 2D interaction diagrams with PoseView to visualize molecular interactions.
• Protein-Protein Interface Classification: Applies HyPPI to classify interfaces between interacting proteins.
• Automatic Pocket Detection and Druggability Assessment: Detects binding pockets and assesses druggability with DoGSiteScorer.
• Enhanced Protein-Ligand Interaction Tools: Provides StructureProfiler for ligand validation, WarPP for water placement, and METALizer for metal ion prediction.
• Keyword Search Functionality: Enables structure searches without requiring PDB codes.
• REST Service Integration: Exposes tools via a REST service for integration into computational pipelines.

Scientific Applications:

• Drug discovery: Supports identification and assessment of binding pockets, ligand validation, and interaction analysis for small-molecule discovery.
• Crop science: Facilitates structure-based analyses relevant to plant proteins and ligand interactions.
• Biotechnology: Enables structural assessment and interface classification for protein engineering and biotechnological applications.

Methodology:

Computational methods explicitly include EDIA-based structure quality scoring, Protoss hydrogen placement, SIENA conformer search, PoseView 2D interaction diagram generation, HyPPI interface classification, DoGSiteScorer pocket detection and druggability scoring, StructureProfiler ligand validation, WarPP water placement, METALizer metal ion prediction, and REST-based access to these tools operating on PDB structures.