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Protein Structure Classification Using Geometric Invariants and Dynamic Programming

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Classification of newly determined protein structures is important in understanding their function and mechanism of action. Currently available methods employ a global structure alignment strategy and are computationally expensive. We propose a two-step methodology with a quick screen to significantly reduce the number of candidate structures followed by global structure alignment of the query structure with the reduced set. We represent a protein structure as a sequence of local structures, codified in the form of geometric invariants. Geometric invariants are quantities that remain unchanged under transformations such as translation and rotation. Protein structures represented as multi-attribute sequences are aligned via dynamic programming to identify close neighbors of the query structure. The query structure is then compared with this reduced dataset using conventional structure comparison methods to predict its functional class. For a typical protein structure, the screening method was able to reduce the protein data bank to mere 200 proteins while preserving structurally closest neighbor in the reduced set. This has resulted in 30 to 60 fold improvement in the execution time. We present the results of leave-one-out classification experiment on ASTRAL-95 domains and comparison with SCOP classification hierarchy.

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Keywords: Nearest neighbor classification; affine gap penalty; cosine similarity; protein structure alignment

Document Type: Research Article

Publication date: 2007-07-01

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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