Dear Modellers,
I am working on a structural alignment between 6 protein structures with an average seq. identity of approx. 25 % and average homology of approx. 45 %. Usage of default values for gap creation and extension penalties for structure/structure superposition (0.0 and 1.75 respecrtively) result in the introduction of multiple (relatively) large gaps in the multiple sequence alignment. Of course I can "avoid" this by increasing both gap creation and extension penalties, but what I would like to know which penalty values are "reasonable" in this case.
Thanking you in advance and with kind regards,
Chris de Graaf
-- drs. C. de Graaf LACDR - Division Molecular Toxicology Department Pharmacochemistry Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam Tel. (31) 020-4447608 Fax. (31) 020-4447610