Abstract
In this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that can pass through the deformed tunnel. By using the two types of graphs corresponding to amino acids and their side chain rotamers, the suggested algorithm classifies amino acids and rotamers which possibly have collisions. Based on the divide and conquer technique, local side chain conformations are computed first, and then a global conformation is generated by combining them. With the exception of certain cases, experimental results show that the algorithm finds up to 327,680 valid side chain conformations from 128~1233 conformation candidates within three seconds.
Highlights
Tunnels and channels in a protein molecule are the pathways for ligands.The ligands are able to move from outside to inside cavity of the molecule or pass through the molecule by using the tunnels or channels
For the protein molecule with side chain flexibility, we suggest an algorithm to compute valid conformational variations for the amino acid side chain rotamers composing a tunnel
A novel algorithm to find every valid conformation for the side chain rotamers in
Summary
Tunnels and channels in a protein molecule are the pathways for ligands (or substrates). The ligands are able to move from outside to inside cavity of the molecule or pass through the molecule by using the tunnels or channels. When a ligand reaches to the cavity, they can interact with residues in the protein molecule, where it causes functions of the protein. A channel is a pathway with two entrances from the exterior to the inside, while a tunnel has only one entrance. It is important to find them through which the ligand passes in a protein. In the remaining part of this paper, we will use the term tunnels, rather than using the term tunnels and channels
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