[RASMB] Partial specific volume of nucleotides

[Mattia Rocco]

Hello everybody,

as you might know, together with Bo Demeler and Emre Brookes we are 
preparing the beta-version release of the UltraScan-SOMO software package 
for biomacromolecular bead modeling starting from high-resolution 
structures. Together with the program we will distribute user-editable 
tables containing the definition of residues found in PDB files, tables 
that are needed for proper SOMO operation. One of the fields in the 
residues definition table is the partial specific volume, used to compute 
the psv of the structure under examination (which can nevertheless be 
overridden by entering, say, an experimental value).

While the values for amino acids and carbohydrate residues, for instance, 
are well defined, this is apparently not the case for ribo and 
deoxyribonucleic acids. Nevertheless, we would like to enter a reasonable 
value for each of the standard four ribonucleosides and ribonucleotides 
(that is, without and with the phosphate) and they deoxy counterparts.

We would therefore appreciate if you could either provide such psv values 
to me (with proper references, please), or indicate to me where to find 
such information.

Many thanks in advance, and happy 2009!

Mattia



Dr. Mattia Rocco
Biopolimeri e Proteomica
Istituto Nazionale per la Ricerca sul Cancro (IST)
c/o Centro per le Biotecnologie Avanzate (CBA)
IST c/o CBA, Largo Rosanna Benzi 10
I-16132 Genova, Italy

Phone: +39-0105737-310
Fax: +39-0105737-325
e-mail: mattia.rocco at istge.it