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Cross-Modal Multivariate Pattern Analysis

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Published on: November 9, 2011

A polynomial-time algorithm for the matching of crossing contact-map patterns.

¹Wilhelm-Schickard Institut für Informatik, Universität Tübingen, Sand 13, D-72076 Tübingen, Germany. gramm@informatik.uni-tuebingen.de

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|October 21, 2006

Summary

We developed a polynomial-time algorithm for Contact Map Pattern Matching (CMPM) on specific {precedes, crosses}-structured patterns. This efficiently finds structural motifs in proteins, answering a key computational biology question.

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Area of Science:

Computational Biology
Bioinformatics
Structural Biology

Background:

Contact maps model protein structures by representing amino acid proximity.
Contact Map Pattern Matching (CMPM) seeks to identify structural motifs within these maps.
General CMPM is computationally challenging (NP-hard).

Purpose of the Study:

To investigate the computational complexity of CMPM for {precedes, crosses}-structured patterns.
To develop an efficient algorithm for this specific CMPM variant.
To resolve an open question regarding the polynomial-time solvability of this problem.

Main Methods:

Developed a novel algorithm for CMPM.
Analyzed the algorithm's time complexity, achieving O(/A/6/Ap/2).
Focused on patterns where arcs are disjoint or crossing ({precedes, crosses}-structured).

Main Results:

Demonstrated that CMPM for {precedes, crosses}-structured patterns is solvable in polynomial time.
The algorithm runs in O(/A/6/Ap/2) time.
Experimental results show efficient processing of real protein contact maps.

Conclusions:

The study provides a polynomial-time solution for a specific, biologically relevant CMPM problem.
This contrasts with the NP-hardness of related problems, offering significant computational advantages.
The findings facilitate efficient identification of structural motifs in proteins.