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Solvent accessible surface representation in a database system for protein docking

T Seidl¹, H P Kriegel

¹Institute for Computer Science, University of Munich, Germany.

Proceedings. International Conference on Intelligent Systems for Molecular Biology

|January 1, 1995

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This study introduces a novel database architecture for protein docking queries, utilizing a topology-based molecular surface representation and the space-efficient TriEdge data structure. This approach enhances the efficiency of molecular database retrieval for complex docking simulations.

Area of Science:

Computational Biology
Database Systems
Structural Bioinformatics

Background:

Protein docking is crucial for understanding molecular interactions but poses significant computational challenges for database querying.
Existing methods often struggle with the geometric and topological complexity of molecular structures.

Purpose of the Study:

To develop an efficient architecture for processing protein docking queries in molecular databases.
To introduce a novel data structure for representing molecular surfaces and supporting topological queries.

Main Methods:

Utilized a multistep query processing paradigm adapted from spatial databases.
Defined a topology-based molecular surface representation.
Proposed and implemented the TriEdge data structure for efficient topological querying and space optimization.

Related Experiment Videos

Compared TriEdge with traditional planar graph representations like the quad-edge structure.

Main Results:

The TriEdge structure offers a significant space reduction (factor of four) compared to quad-edge structures.
The proposed architecture efficiently supports docking queries by integrating geometric and physicochemical parameters.
Demonstrated the feasibility and performance of the TriEdge structure through prototype investigation.

Conclusions:

The developed architecture and TriEdge data structure provide an efficient solution for protein docking queries in molecular databases.
This approach enhances retrieval speed and reduces storage requirements for complex molecular data.
The topology-based surface representation is key to effectively handling molecular geometry in docking applications.