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Flexible structural comparison allowing hinge-bending, swiveling motions
G Verbitsky1, R Nussinov, H Wolfson
1Computer Science Department, School of Mathematical Sciences, Tel Aviv University, Israel.
Proteins
|February 18, 1999
Summary
This study introduces a fast, automated method for comparing protein structures, treating them as flexible objects with swiveling parts. The technique efficiently identifies structural motifs with hinges, improving upon rigid-body comparison methods.
Area of Science:
- Structural biology
- Bioinformatics
- Computational chemistry
Background:
- Current protein structure comparison methods treat molecules as rigid.
- Identifying flexible protein structures with hinge regions is challenging.
- Existing methods require predefined motifs or extensive conformational searches.
Purpose of the Study:
- To develop an efficient and automated method for flexible protein structure comparison.
- To enable the detection of hinge-bent structural motifs in proteins.
- To overcome limitations of rigid-body comparison approaches.
Main Methods:
- Developed a novel algorithm that treats proteins as articulated objects with swiveling parts.
- Allowed rigid sub-parts to rotate around defined swiveling points during comparison.
- Algorithm complexity is O(n^2), independent of amino acid order.
Main Results:
- The method efficiently detects structural motifs with hinges between domains.
- Successfully identified known hinge-bent domains/motifs in proteins with domain movements.
- Detected additional structural matches beyond known motifs.
Conclusions:
- The presented algorithm is a highly efficient, fully automated tool for flexible protein structure comparison.
- This approach significantly advances the identification of hinge-bending movements in proteins.
- The method offers a fast alternative to conformational space searches for structural motif discovery.