NDLI: RNA Secondary Structure Prediction in the Presence of Single-Stranded Binding Proteins

Content Provider	IEEE Xplore Digital Library
Author	Forties, R.A. Bundschuh, R.
Copyright Year	2009
Abstract	Secondary structure prediction of RNA molecules is a problem in Bioinformatics with several well established solutions. However, while the approaches to RNA secondary structure prediction are successful in describing RNA molecules in vitro, RNA molecules in vivo often assume their secondary structure while interacting with many other consitutents of the cell. One of those constitutents that have the ability to significantly alter RNA secondary structure formation are proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV or the RecA DNA repair protein in bacteria. We extend established secondary structure prediction methods to explicitly include the effect of such interactions. Using our model we are able to predict the probability of proteins binding at any position in the nucleic acid sequence as well as the impact of the protein on nucleic acid base pairing and on the end-to-end distance distribution of the nucleic acid.
Starting Page	57
Ending Page	57
File Size	82512
Page Count	1
File Format	PDF
ISBN	9780769536859
DOI	10.1109/OCCBIO.2009.17
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-06-15
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins In vivo Microorganisms RNA DNA Prediction methods Predictive models Human immunodeficiency virus Bioinformatics In vitro
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
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