Types of Comparisons
Because protein structures are composed of amino acids whose side chains are linked by a common protein backbone, a number of different possible subsets of the atoms that make up a protein macromolecule can be used in producing a structural alignment and calculating the corresponding RMSD values. When aligning structures with very different sequences, the side chain atoms generally are not taken into account because their identities differ between many aligned residues. For this reason it is common for structural alignment methods to use by default only the backbone atoms included in the peptide bond. For simplicity and efficiency, often only the alpha carbon positions are considered, since the peptide bond has a minimally variant planar conformation. Only when the structures to be aligned are highly similar or even identical is it meaningful to align side-chain atom positions, in which case the RMSD reflects not only the conformation of the protein backbone but also the rotameric states of the side chains. Other comparison criteria that reduce noise and bolster positive matches include secondary structure assignment, native contact maps or residue interaction patterns, measures of side chain packing, and measures of hydrogen bond retention.
Read more about this topic: Structural Alignment
Famous quotes containing the words types of, types and/or comparisons:
“Our children evaluate themselves based on the opinions we have of them. When we use harsh words, biting comments, and a sarcastic tone of voice, we plant the seeds of self-doubt in their developing minds.... Children who receive a steady diet of these types of messages end up feeling powerless, inadequate, and unimportant. They start to believe that they are bad, and that they can never do enough.”
—Stephanie Martson (20th century)
“... there are two types of happiness and I have chosen that of the murderers. For I am happy. There was a time when I thought I had reached the limit of distress. Beyond that limit, there is a sterile and magnificent happiness.”
—Albert Camus (1913–1960)
“I don’t like comparisons with football. Baseball is an entirely different game. You can watch a tight, well-played football game, but it isn’t exciting if half the stadium is empty. The violence on the field must bounce off a lot of people. But you can go to a ball park on a quiet Tuesday afternoon with only a few thousand people in the place and thoroughly enjoy a one-sided game. Baseball has an aesthetic, intellectual appeal found in no other team sport.”
—Bowie Kuhn (b. 1926)