NDLI: Validating the Network-Based Objective Measure for Helical Membrane Protein Structures

Content Provider	IEEE Xplore Digital Library
Author	Jun Gao Zhijun Li
Copyright Year	2010
Abstract	Computational structure prediction, including de novo and homology modeling, is an important tool for membrane protein studies. Developing an accurate scoring function that can be used for structure discrimination and assessment remains a challenge. In our previous work, we have analyzed a set of high-resolution membrane protein structures using the network approach developed in our lab and proposed such a scoring function. Here, we aimed to validate this function using three diverse datasets. First, we applied it to a diverse set of 139 homology models. The models included in this dataset represent ten unique membrane protein superfamilies and have 20-100% sequence identity to their respective templates. Next, this scoring function was adopted for the analysis of nine bacteriorhodopsin structures of different resolution. Finally, the discrimination capability of the proposed scoring function was tested using the HOMEP benchmark dataset of 92 membrane protein models. Detailed analyses of the results confirmed that the proposed network measure can be adopted as an objective packing quality indicator and for structure discrimination. These results suggested that the proposed scoring function is a good indicator of high-quality models and can be applied to a variety of membrane protein models.
Starting Page	1
Ending Page	4
File Size	364550
Page Count	4
File Format	PDF
ISBN	9781424447121
ISSN	21517622
DOI	10.1109/ICBBE.2010.5516239
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-06-18
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Drugs Computer science Protein engineering Chemistry Amino acids Frequency Biomembranes Electronic mail Bioinformatics Assembly
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
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
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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