NDLI: Efficient retrieval of electron density patterns for modeling proteins by X-ray crystallography

Content Provider	IEEE Xplore Digital Library
Author	Gopal, K. Romo, T.D. Sacchettini, J.C. Ioerger, T.R.
Copyright Year	2004
Abstract	Inefficient case retrieval is a major problem in many case-based reasoning systems, especially when case matching is expensive and the case-base is large. In this paper, we present a two-phase approach where an inexpensive feature-based method is used to jind a set of potential matches and a more expensive and accurate case matching method is used to make the jinal selection. This approach has been successfully employed in TEXTALTM, a system that retrieves previously solved 3D patterns of electron density from a database to determine the structure of proteins. Electron density patterns are characterized by numeric features and an appropriate distance measure is used to efficiently jilter good matches through an exhaustive search of the database. These matches are then examined using a computationally expensive density correlation procedure based on jinding an optimal superposition between 3D patterns. We provide an empirical and theoretical analysis of some of the keys issues related to this method. In particular, we dejine a model for estimating how approximate various featurebased similarity measures are (relative to an objective matching metric), and determine its relation to the number of cases that should be jiltered from a given database to make the approach effective.
Starting Page	380
Ending Page	387
File Size	218078
Page Count	8
File Format	PDF
ISBN	0780388232
DOI	10.1109/ICMLA.2004.1383539
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2004-12-16
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Computer science Matched filters Databases Predictive models Information retrieval Particle measurements Crystallography Pattern matching Electrons
Content Type	Text
Resource Type	Article

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