NDLI: Database Approaches and Data Representation in Structural Bioinformatics

Content Provider	IEEE Xplore Digital Library
Author	Gopal, K. Sacchettini, J.C. Ioerger, T.R.
Copyright Year	2007
Description	Author affiliation: Texas A&M Univ, College station (Gopal, K.)
Abstract	Database approaches are widely used in structural bioinformatics, since ab initio techniques are often computationally prohibitive, and the structure of biological macromolecules are typically derived from a limited set of motifs. There are several issues and challenges that arise when developing methods to enable efficient database retrieval. For example, how can complex data be represented efficiently, and what should be the size and composition of the database? In this work, we discuss some of these challenges, based on a crystallographic protein model-building program called TEXTAL. In particular, we discuss how structural information on amino acids is represented (as numeric features), how difficult it is to recognize amino acids (based on 3D electron density patterns), and what types of examples (and how many of them) need to be stored in the database. These insights are potentially useful in many other related applications, such as structure-based drug design, protein-protein interaction, discriminating nucleic acids and proteins in hybrid complexes, etc.
Starting Page	425
Ending Page	432
File Size	2443536
Page Count	8
File Format	PDF
ISBN	9781424415090
DOI	10.1109/BIBE.2007.4375597
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-10-14
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Bioinformatics Proteins Spatial databases Amino acids Biology computing Molecular biophysics Information retrieval Crystallography Pattern recognition Electrons features structural bioinformatics X-ray crystallography electron density map interpretation
Content Type	Text
Resource Type	Article

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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
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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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