Journal of Molecular Biology
An Assessment of Amino Acid Exchange Matrices in Aligning Protein Sequences: The Twilight Zone Revisited
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2016, Computational Biology and ChemistryCitation Excerpt :As a consequence of multiplication, with this way of encoding is possible loss of information regarding the separation of positive and negative sets for an AA that often occurs in one of the two sets and which has a negative score for substitution. In order to suppress whether such cases occurred in our models, instead of the standard BLOSUM62 matrix, we used VOGG matrix (Vogt et al., 1995) the modification of the BLOSUM62 matrix which has only positive values. In this way, all cases are separated without loss of information because by multiplying with positive values the ratio of frequencies does not change.
Optimization techniques in molecular structure and function elucidation
2009, Computers and Chemical EngineeringCitation Excerpt :Structural alignment (Bourne & Shindyalov, 2003) has been emerging recently as a technique that provides even more meaningful information for comparing proteins than sequence-based approaches. In fact, structural alignment is now used to assess various sequence alignment methods (Orengo et al., 1997; Vogt, Etzold, & Argos, 1995). Qualitatively, the structural alignment problem requires assigning amino acid residues of a given protein to amino acid residues of another given protein, in a way that highlights similarities between the two proteins.
Factors influencing estimates of coordinate error for molecular replacement
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