NDLI: Prediction of Metal Ion–Binding Sites in Proteins Using the Fragment Transformation Method

Content Provider	PubMed Central
Author	Lu, Chih-hao Lin, Yu-feng Lin, Jau-ji Yu, Chin-sheng
Editor	Vertessy, Beata G.
Copyright Year	2012
Abstract	The structure of a protein determines its function and its interactions with other factors. Regions of proteins that interact with ligands, substrates, and/or other proteins, tend to be conserved both in sequence and structure, and the residues involved are usually in close spatial proximity. More than 70,000 protein structures are currently found in the Protein Data Bank, and approximately one-third contain metal ions essential for function. Identifying and characterizing metal ion–binding sites experimentally is time-consuming and costly. Many computational methods have been developed to identify metal ion–binding sites, and most use only sequence information. For the work reported herein, we developed a method that uses sequence and structural information to predict the residues in metal ion–binding sites. Six types of metal ion–binding templates– those involving Ca2+, Cu2+, Fe3+, Mg2+, Mn2+, and Zn2+–were constructed using the residues within 3.5 Å of the center of the metal ion. Using the fragment transformation method, we then compared known metal ion–binding sites with the templates to assess the accuracy of our method. Our method achieved an overall 94.6 % accuracy with a true positive rate of 60.5 % at a 5 % false positive rate and therefore constitutes a significant improvement in metal-binding site prediction.
Related Links	http://dx.doi.org/10.1371/journal.pone.0039252
Starting Page	39252
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	6
Volume Number	7
Language	English
Publisher	Public Library of Science
Publisher Date	2012-06-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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