CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Comparing 3D Protein Structures Similarity by Using Fractal Features
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
PSIST: Indexing Protein Structures Using Suffix Trees
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
PSIST: A scalable approach to indexing protein structures using suffix trees
Journal of Parallel and Distributed Computing
Towards Efficient Searching on the Secondary Structure of Protein Sequences
Fundamenta Informaticae - Special issue ISMIS'05
Geometric suffix tree: Indexing protein 3-D structures
Journal of the ACM (JACM)
Geometric suffix tree: a new index structure for protein 3-d structures
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
ISMIS'05 Proceedings of the 15th international conference on Foundations of Intelligent Systems
Towards Efficient Searching on the Secondary Structure of Protein Sequences
Fundamenta Informaticae - Special issue ISMIS'05
Indexing methods for efficient protein 3D surface search
Proceedings of the ACM sixth international workshop on Data and text mining in biomedical informatics
Fast protein 3D surface search
Proceedings of the 7th International Conference on Ubiquitous Information Management and Communication
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In this paper, we present a novel indexing method calledProtDex to facilitate fast searching in 3-dimensional proteinstructure database. In ProtDex, we first build an index onthe representative properties of all proteins in the database.When evaluating a query, with the help of the index, we filterout a small candidate list of proteins. Then, we can eitherdirectly report them, with their respective rankings, to theuser, or do the expensive actual alignments on them uponuser's request. Preliminary experimental results show thatour solution is up to 16 times faster than the popular DALImethod for database sear hing task (without actual alignments), while its overall accuracy is only slightly inferiorto that of DALI. The software is available upon request bysending emails to the authors.