Topology Data Bank of Transmembrane Proteins

Topology Data Bank of Transmembrane Proteins provides a curated repository of experimentally derived topology annotations and HMMTOP-predicted transmembrane topologies to support structural interpretation of membrane protein organization.

Key Features:

• Experimental topology annotations: Contains experimentally derived topology information for over a thousand transmembrane proteins.
• HMMTOP prediction: Applies the HMMTOP transmembrane topology prediction algorithm to compute most probable topologies consistent with experimental constraints.
• Structural integration: Integrates topology data with structural information from the Protein Data Bank (PDB) and PDBTM.
• Rich annotation: Annotates entries with protein sequence, name, organism, and cross-references to other databases.
• Data sources: Aggregates curated data from literature sources and publicly available databases.

Scientific Applications:

• Structural biology: Supports interpretation and analysis of membrane protein topology in structural studies.
• Drug design: Provides topology information relevant to targeting membrane proteins in drug discovery.
• Functional analysis: Aids understanding of membrane protein function through annotated topology data.
• Data integration: Bridges sequence database coverage and available experimental or computational topology information.

Methodology:

Data are compiled from literature and public databases, integrated with PDB and PDBTM structural information, and processed with the HMMTOP transmembrane topology prediction algorithm constrained by experimental annotations.