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Detailed atomistic molecular models have been developed with the help of molecular mechanics and semi-empirical quantum mechanical calculations using Cerius and MOPAC V6.0 program packages and structural, volumetric, and mechanical properties, e.g. geometrical values, densities, have been calculated by simulations on these models.
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The DNA packaging and structural modules extend from MAV_0795 to MAV_0813.
The module containing DNA packaging and structural proteins is the largest module of the Sf101 phage, and is predicted to contain 15 orfs (orf 1 to 15).
The packaging and structural proteins (Gp1-Gp19) are generally very well conserved, with high sequence similarities between all three phages, ranging from 89.7%to99.3%3% amino acid identity (see Figure 1 and additional file 2) with one exception - gp19.
The first part of the genome encodes proteins mainly involved in DNA packaging (terminases) and structural proteins; several of the proteins have been experimentally verified to be produced by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry [ 34].
In this work, we introduce a Perl-based software pipeline that integrates multiple free software packages to predict protein structures and structural properties [19].
The modelling approach is based on an iterative algorithm for automated target-to-template alignment followed by model building using the MODELLER program [45] integrated in the M4T package and subsequent structural optimization of the obtained model.
But workers have warned that their campaign against the stringent package of fiscal policies and structural reforms will be ongoing and relentless.
11.59am BST Greek finance minister still optimistic Over to Greece where our correspondent Helena Smith has the latest on the on-off talks over the bumper, €13.5bn package of budget cuts and structural reforms that are key to the euro zone's weakest link receiving further rescue funds.
Next, we tried out several different sequence alignment and structural superposition software packages to align the entire proteins.
As such, some limited putative commonalities exist on the DNA sequence and structural level between packaging of prokaryotic and eukaryotic chromosomes [43].
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