Sentence examples for using a probe radius from inspiring English sources

To calculate the solvent accessible surface, each of the nine regions were selected separately and calculations were performed by the method of Connolly, using a probe radius of 1.40 A° [15], [16].

As mentioned in the section on Protocol for each of the 20 residue types we have analyzed the relationship between percentage solvent accessibility calculated from full-atom models using a probe radius of 1.4Å and ASA of Cα atom from Cα-only structures for a probe radius of 3.5Å.

Accessible surface area (expressed in square Angstroms) of a Cα atom corresponding to a specific residue, calculated using a specific probe radius in a given protein structure, is compared to accessibility value (expressed as %) of the same residue calculated using all the available atomic positions and using a probe radius of 1.4Å.

Solvent-accessible surfaces were generated in DS Visualizer version 2.0 (Accelrys, USA) using a probe radius of 1.7 Å. Electrostatic surface potential was calculated by assigning partial charges to all heavy atoms and applying a distance cut-off of 12.5 Å for mapping charges (red for negative and blue for positive) to the molecular surfaces.

Molecular surface was constructed using the dms program inbuilt in UCSF's Chimera using a probe radius of 1.4 Å.

The potential ligand binding sites were generated using a probe radius of 5.0 Å and the binding site having highest z-score was considered for further investigation.

However, this was partly because we used a probe radius of 3 Å to construct the overall shape of the protein, and therefore we only detected channels below this radius.

All calculations used a probe radius of 1.4 Å, which roughly corresponds to the size of a water molecule.

To estimate the experimentally calculated RSA, we used a probe radius of 2Å, as also used by Beuming and Weinstein (2004) to emulate the -CH2- group in the lipid environment.

The area was calculated using a probe with a radius of 1.4 Å.

Our approach to recognize solvent exposed and buried residues based solely on Cα positions involves calculation of accessible surface area values of Cα using a probe sphere of appropriate radius.