Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory.

ABSTRACT: The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to

SUBMITTER: Uporov IV 

PROVIDER: S-EPMC4613251 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature