Amino acids pattern-biased spiral search for protein structure prediction
Author(s)
Rashid, Mahmood A
Polash, Md Masbaul Alam
Newton, MA Hakim
Hoque, Md Tamjidul
Sattar, Abdul
Year published
2014
Metadata
Show full item recordAbstract
Proteins are essentially sequences of amino acids. They adopt specific folded 3-dimensional structures to perform specific tasks. The formation of 3-dimensional structures is largely guided by the constituent amino acids. Therefore, the positional presence of amino acids in a sequence might play important roles during the protein folding process. In this paper, we present a new heuristic derived from the positional patterns of amino acids in a sequence. With the help of a biased tabu tenure, we apply this heuristic within a spiral search algorithm. The spiral search is an efficient algorithm to develop hydrophobic core in a ...
View more >Proteins are essentially sequences of amino acids. They adopt specific folded 3-dimensional structures to perform specific tasks. The formation of 3-dimensional structures is largely guided by the constituent amino acids. Therefore, the positional presence of amino acids in a sequence might play important roles during the protein folding process. In this paper, we present a new heuristic derived from the positional patterns of amino acids in a sequence. With the help of a biased tabu tenure, we apply this heuristic within a spiral search algorithm. The spiral search is an efficient algorithm to develop hydrophobic core in a protein structure pulling hydrophobic amino acids towards the core centre in a spiral fashion. On a set of standard benchmark proteins, we experimentally show that applying our new heuristic improves the performance of a spiral search algorithm consistently.
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View more >Proteins are essentially sequences of amino acids. They adopt specific folded 3-dimensional structures to perform specific tasks. The formation of 3-dimensional structures is largely guided by the constituent amino acids. Therefore, the positional presence of amino acids in a sequence might play important roles during the protein folding process. In this paper, we present a new heuristic derived from the positional patterns of amino acids in a sequence. With the help of a biased tabu tenure, we apply this heuristic within a spiral search algorithm. The spiral search is an efficient algorithm to develop hydrophobic core in a protein structure pulling hydrophobic amino acids towards the core centre in a spiral fashion. On a set of standard benchmark proteins, we experimentally show that applying our new heuristic improves the performance of a spiral search algorithm consistently.
View less >
Conference Title
PRICAI 2014: TRENDS IN ARTIFICIAL INTELLIGENCE
Volume
8862
Publisher URI
Subject
Artificial intelligence not elsewhere classified
Information and computing sciences