ChannelsDB 2.0

ChannelsDB 2.0 catalogs structural annotations of protein channels, including tunnels and pores, in biomacromolecular structures from the Protein Data Bank and AlphaFoldDB to support analysis of channel geometry, physico-chemical properties, and mutation impacts.

Key Features:

• Expanded Database Content: Approximately 4.6× increase in channel annotations as of September 1, 2023, incorporating entries from PDB and AlphaFoldDB.
• Integration with Multiple Tools: Channel detections and annotations combine calculations from CAVER with data obtained via the original MOLE tool.
• Inclusion of AlphaFill Data: Incorporates tunnels that start from cofactors within the AlphaFill database to extend coverage to AlphaFold/UniProt-based models.
• Detailed Structural Information: Stores geometric channel features such as length and radius along with physico-chemical properties derived from channel-lining amino acids.
• Interlinking with UniProt Mutation Data: Links channel annotations to UniProt mutation annotation data to enable correlation of structural features with genetic variants.

Scientific Applications:

• Structural Biology: Comparative and detailed analysis of protein channel architecture, including tunnels and pores, in experimental and predicted structures.
• Molecular Dynamics and Simulation: Provision of geometric and physico-chemical channel parameters for setup and interpretation of molecular dynamics and modeling studies.
• Drug Design and Discovery: Structural channel data support identification of channel-related drug targets and design of compounds that modulate channel access or activity.
• Genetic Research: Correlation of channel structural features with UniProt mutation annotations to investigate effects of genetic variation on channel function.

Methodology:

Channel annotations derive from MOLE and CAVER calculations; tunnels from AlphaFill are included when starting from cofactors; stored data include channel length, radius, and physico-chemical properties from channel-lining amino acids; annotations are interlinked with UniProt mutation data.