Calculation of protein domain structural similarity using two-dimensional representations.
By reducing protein structures to two-dimensional representations, it is possible to speed up the alignment of the structures and hence calculate similarity indices faster that using three-dimensional representations. Using amino acid based representations gives much better discrimination between proteins and faster calculations. Taking into account the relative similarity of the amino acids involved allowed improved accuracy at very little time cost.
Allen
Benjamin C P
BC
Central Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QH, United Kingdom.
Grant
Guy H
GH
Richards
W Graham
WG
D000596:Amino Acids / Q000737:chemistry; D001699:Biometry; D008956:Models, Chemical; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins