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3-D lookup: fast protein structure database searches at 90% reliability

L Holm¹, C Sander

¹European Molecular Biology Laboratory, Heidelberg, Germany.

Proceedings. International Conference on Intelligent Systems for Molecular Biology

|January 1, 1995

Summary

A new heuristic method rapidly identifies 3-D protein structure similarities. This approach offers a reliable and fast preprocessor for protein structure database searches.

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Area of Science:

Structural bioinformatics
Computational biology
Biochemistry

Background:

Detecting three-dimensional (3-D) protein structure similarities is computationally challenging (NP-complete).
Existing methods often use bottom-up approaches, building alignments from local matches.
Fewer protein fold classes exist compared to sequence families, highlighting the importance of structural comparison.

Purpose of the Study:

To develop a novel heuristic for efficiently identifying 3-D similarities between protein structures.
To provide a fast and reliable method for querying protein structure databases.

Main Methods:

A top-down approach starting with global comparison of protein structures.
Utilizing a fast 3-D lookup of secondary structure motifs for initial superimposition.
Employing an iterative dynamic programming step to extend alignments of C-alpha atoms.

Main Results:

The heuristic method successfully identifies 3-D similarities between query structures and a database.
An all-against-all comparison of 385 proteins (150,000 pairs) was completed in one day on a single processor.
Individual query structure searches against the database take only minutes.
The method demonstrates 90% reliability in capturing statistically significant structural similarities.

Conclusions:

The novel heuristic provides a rapid and reliable method for 3-D protein structure comparison.
This approach serves as an effective preprocessor for comprehensive protein structure database searches.
The top-down strategy offers an efficient alternative to traditional bottom-up alignment methods.

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