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Recognition of Structure Similarities in Proteins

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Abstract

Protein fold structure is more conserved than its amino acid sequence and closely associated with biological function, so calculating the similarity of protein structures is a fundamental problem in structural biology and plays a key role in protein fold classification, fold function inference, and protein structure prediction. Large progress has been made in recent years in this field and many methods for considering structural similarity have been proposed, including methods for protein structure comparison, retrieval of protein structures from databases, and ligand binding site comparison. Most of those methods can be available on the World Wide Web, but evaluation of all the methods is still a hard problem. This paper summarizes some popular methods and latest methods for structure similarities, including structure alignment, protein structure retrieval, and ligand binding site alignment.

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Authors and Affiliations

  1. Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China

    Lin WANG, Yuqing QIU, Jiguang WANG & Xiangsun ZHANG

  2. Graduate School of the Chinese Academy of Sciences, Beijing, 100049, China

    Lin WANG, Yuqing QIU & Jiguang WANG

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  1. Lin WANG
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  2. Yuqing QIU
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  3. Jiguang WANG
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  4. Xiangsun ZHANG
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Correspondence to Lin WANG.

Additional information

This research is supported by the National Natural Science Foundation of China under Key Research Grant No. 10631070, and JSPS and NSFC under JSPS-NSFC Collaboration Project under Grant No. 10711140116.

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WANG, L., QIU, Y., WANG, J. et al. Recognition of Structure Similarities in Proteins. J Syst Sci Complex 21, 665–675 (2008). https://doi.org/10.1007/s11424-008-9143-5

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  • DOI: https://doi.org/10.1007/s11424-008-9143-5

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