IBiSS

IBiSS integrates sequence and three-dimensional structural data to enable analysis of conserved residues, catalytic sites, and protein–protein interfaces in large macromolecular complexes derived from X-ray crystallography and cryo-electron microscopy (cryo-EM).

Key Features:

• Simultaneous Structure-Sequence Analysis: Maps multiple sequence alignments onto three-dimensional structures to identify conserved residues involved in catalysis and protein–protein interfaces.
• Pre-aligned Internal Database: Maintains a pre-aligned collection of multiple sequences across species linked to three-dimensional structural information for rapid retrieval.
• Automated Annotation Updates: Retrieves and updates annotations automatically from UniProt, the Protein Data Bank (PDB), and the Electron Microscopy Data Bank (EMDB).
• Comprehensive Structural Coverage: Includes structural data for ribosomes, RNA polymerases, nucleosomes, proteasomes, and photosystem I and II complexes.
• Support for Crystallography and Cryo-EM: Handles structures derived from X-ray crystallography and cryo-electron microscopy (cryo-EM).

Scientific Applications:

• Conserved Residue and Interface Analysis: Facilitates identification of residues critical for catalysis and protein–protein interactions within macromolecular complexes.
• Transcription and Translation Studies: Supports analysis of ribosomes and RNA polymerases to investigate mechanisms of transcription and translation.
• DNA Packaging and Protein Degradation Research: Enables study of nucleosomes and proteasomes to investigate DNA packaging and protein degradation mechanisms.
• Photosynthesis Complex Analysis: Supports sequence and structural investigation of photosystem I and II to study photosynthetic mechanisms.
• Evolutionary and Comparative Analyses: Enables cross-species comparison of sequence alignments and structures to elucidate evolutionary relationships and functional adaptations.

Methodology:

An internal database of sequences pre-aligned across species is linked to three-dimensional structural information; annotations are automatically retrieved and updated from UniProt, PDB, and EMDB; sequences are mapped onto 3D structures from X-ray crystallography and cryo-EM.