Paper Info
Title
PROuST: a comparison method of three-dimensional structures of proteins using indexing techniques.
Abstract
We present a new method for protein structure comparison that combines indexing and dynamic programming (DP). The method is based on simple geometric features of triplets of secondary structures of proteins. These features provide indexes to a hash table that allows fast retrieval of similarity information for a query protein. After the query protein is matched with all proteins in the hash table producing a list of putative similarities, the dynamic programming algorithm is used to align the query protein with each protein of this list. Since the pairwise comparison with DP is applied only to a small subset of proteins and, furthermore, DP reuses information that is already computed and stored in the hash table, the approach is very fast even when searching the entire PDB. We have done extensive experimentation showing that our approach achieves results of quality comparable to that of other existing approaches but is generally faster.
Year
DOI
Venue
2004
10.1089/cmb.2004.11.1061
JOURNAL OF COMPUTATIONAL BIOLOGY
Keywords
Field
DocType
protein structure comparison,secondary structure,indexing,dynamic programming
Pairwise comparison,Hash tree,Double hashing,Computer science,Rolling hash,Search engine indexing,Algorithm,Hash function,Artificial intelligence,Dynamic perfect hashing,Machine learning,Hash table
Journal
Volume
Issue
ISSN
11.0
6
1066-5277
Citations 
PageRank 
References 
14
0.95
11
Authors
3
Name
Order
Citations
PageRank
Matteo Comin119120.94
C. Guerra246752.24
Giuseppe Zanotti3262.91