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• W2109922499 abstract "Abstract Motivation: Secondary-Structure Guided Superposition tool (SSGS) is a permissive secondary structure-based algorithm for matching of protein structures and in particular their fragments. The algorithm was developed towards protein structure prediction via fragment assembly. Results: In a fragment-based structural prediction scheme, a protein sequence is cut into building blocks (BBs). The BBs are assembled to predict their relative 3D arrangement. Finally, the assemblies are refined. To implement this prediction scheme, a clustered structural library representing sequence patterns for protein fragments is essential. To create a library, BBs generated by cutting proteins from the PDB are compared and structurally similar BBs are clustered. To allow structural comparison and clustering of the BBs, which are often relatively short with flexible loops, we have devised SSGS. SSGS maintains high similarity between cluster members and is highly efficient. When it comes to comparing BBs for clustering purposes, the algorithm obtains better results than other, non-secondary structure guided protein superimposition algorithms. Availability: SSGS is available for download at Contact: ruthn@ncifcrf.gov Supplementary information: Supplementary data are available at Bioinformatics online." @default.
• W2109922499 created "2016-06-24" @default.
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• W2109922499 date "2006-03-16" @default.
• W2109922499 modified "2023-10-16" @default.
• W2109922499 title "A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly" @default.
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• W2109922499 doi "https://doi.org/10.1093/bioinformatics/btl098" @default.
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