A similarity search algorithm to predict protein structures
journal contribution
posted on 2006-01-01, 00:00authored byJiyuan An, Yi-Ping Phoebe Chen
Accurate prediction of protein structures is very important for many applications such as drug discovery and biotechnology. Building side chains is an essential to get any reliable prediction of the protein structure for any given a protein main chain conformation. Most of the methods that predict side chain conformations use statistically generated data from known protein structures. It is a computationally intractable problem to search suitable side chains from all possible rotamers simultaneously using information of known protein structures. Reducing the number of possibility is a main issue to predict side chain conformation. This paper proposes an enumeration based similarity search algorithm to predict side chain conformations. By introducing “beam search” technique, a significant number of unrelated side chain rotamers can easily be eliminated. As a result, we can search for suitable residue side chains from all possible side chain conformations.
History
Journal
Lecture notes in computer science
Volume
4252
Pagination
1305 - 1312
Location
Berlin, Germany
ISSN
0302-9743
eISSN
1611-3349
Language
eng
Notes
Book: 'Knowledge-Based Intelligent Information and Engineering Systems'