OPM Subset: Non-Redundant High-Resolution Multi-Pass Membrane Protein Structures

A curated subset of PDB structure files from the OPM database, downloaded on February 22, 2023. The files contain alpha-helical integral membrane proteins with at least three transmembrane regions at a resolution better than 2.7 Angstroms. The dataset was curated by Szula Kane of Stockholm University for an MSc thesis project on structural characterization.

Use Cases

• Benchmarking transmembrane region prediction algorithms based on the curated set of high-resolution structures.
• Training machine learning models for protein structure prediction using the non-redundant, high-resolution examples.
• Analyzing structural patterns of consecutive transmembrane helices based on the described selection criteria.
• Studying sequence-structure relationships in integral membrane proteins using the clustered, low-sequence-identity set.

Strengths

• Proteins are filtered for high resolution, with all structures having a resolution better than 2.7 Angstroms.
• The set is non-redundant, with a sequence identity of less than 40% based on clustering with the cd-hit algorithm.
• All proteins are alpha-helical integral membrane proteins with at least three transmembrane regions.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.

Provenance

Source

OPM (Orientations of Proteins in Membranes) database.

Collection Method

Curated subset downloaded from OPM on a specific date.