Flexible mapping of homology onto structure with Homolmapper

BMC Bioinformatics

Table 4 Scoring options for occupancy and B-factor fields with PSSM inputs

Reported Score	Source Matrix
log-odds of query residue	PSSM
observed percentage of query residue	observed-percentages
vector length*	PSSM
vector distance*	PSSM
vector angle*	PSSM
charge	observed-percentages
degen	observed-percentages
sloppy	observed-percentages

PSSM inputs will always result in reporting the consensus residue to the element field. The SegID field can be used to report the information per position or the relative weight versus pseudocounts. Scores marked with an asterisk (*) are calculated by considering each row in the PSSM as a 20-dimensional vector from the origin to the indicated point. The query residue is then considered as a 20-dimensional unit vector normalized to the length of the PSSM vector, and the distance and angle between the two vectors are calculated assuming the space is Euclidean.

ISSN: 1471-2105