Some data about internal/external placement of aminoacids?

VICTOR B. STRELETS STRELETS at SCRI.FSU.EDU
Mon Aug 22 12:13:16 EST 1994


Hi Netters,

Is there (in papers, on FTP sites etc.) some well formalized
information about concrete amino acids placement (internal/external)
in protein globule? Solvent accessability classification could
be appropriate, but it seems to me that this parameter (as well as
functions based on atomic temperature factor B-values, estimations of
local compactness of structure through Ca distance analysis, experimental 
epitope mapping etc.) will be not fully correct. They simply can't take
into account deep cavities, bulbes  and other not so rare constructions
and show rather estimation for probability to find corresponding
amino acid inside space-continuous block of high density (what is
not evean a structural module). Is there somebody who did similar 
classification work manually (using expert rules or something else
even like visual 3D picture inspection)?

Any recomendations, including references on papers containing
aminoacid classifications similar to the requested, will be helpful.
Even references on the accesable data like epitopes placement
will be greatly appreciated (despite differences in asked/answered
questions..).

Thanks,
V.Strelets



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