Sentence examples for modeled proteins was from inspiring English sources

The stereo-chemical quality of modeled proteins was verified by PROCHECK [ 85].

Stability of docking of ligands into the modeled proteins were also investigated using MD simulations.

These modeled proteins were compared (PROCHECK) for the structural parameters including aa ratio in the Ramachandran map, dihedral, covalent and overall.

The evaluated Ramachandran plot for the modeled proteins were also compared to the template proteins (1XCQ and 1 N64) to check the distribution of residues in favored and disallowed regions between each target and template models.

PDB files of the modeled proteins are provided as Additional file 3. Alkanes are ubiquitous in marine and soil environments, occurring as by-products of cell metabolism and death; they also enter the marine environment from natural hydrocarbon seeps and anthropogenic sources.

The interaction of this ligand with modeled protein was performed.

Hence modeled protein was stabilized by MD simulations technique.

The homology modeled protein was inserted into the membrane aligning the helices approximately perpendicular to the membrane surface.

The electrostatic surface potential energy of the modeled protein was calculated using the Adaptive Poisson-Boltzmann solver (APBS) package via PDB2PQR web portal (http://kryptonite.nbcr.net/pdb2pqr/) [ 93].

Raw MFS data for each modeled protein are available as Additional file 5.

The unabridged superimposition of MFS data onto a full ClustalW2 alignment of all modeled Hmd proteins is available as Additional file 6.