We can provide data of three dimensional atomic coordinate, hydrogen bond analysis, and interaction analysis of the protein with ligands, etc., and construct structure data which can be shown in three-dimension.
In ice, these water molecules are connected by weaker hydrogen bonds, so that every oxygen forms two short covalent bonds and two long hydrogen bonds with its neighbouring protons.
A hydroxyl group, for example, can be both a hydrogen bond donor and a hydrogen bond acceptor, and it would be impossible to treat this with a single OH pseudo-atom.
Many of the mutations that cause visual disorders have been identified as mutations of amino acids in the hydrogen bonding moieties that stabilize the gaps between these α-helices.
This may be achieved by the addition of just a few extra hydrogen bonds, an internal salt link or extra internal hydrophobic residues, giving a slightly more hydrophobic core.
The frequency of intramolecular hydrogen bonds can be monitored by a simple algorithm that considers each time step in the simulation and uses a filter to detect hydrogen bonds.
Basics of the molecular recognition of biological materials Interactions of biopolymers are based on the specific recognition of the partner by the use of hydrogen bonds, van der Waals force, etc.
The glucose residues at subsites1-3 forms 8-10 hydrogen bonds with the protein residues. Although the glucose residue at subsite 4 makes only one hydrogen bond with His300, it has many van der Waals contacts with the surrounding hydrophobic residues.
Other helices, such as the 3 10 helix and π helix, are calculated to have energetically favorable hydrogen-bonding patterns but are rarely observed in natural proteins except at the ends of α helices due to unfavorable backbone packing in the center of the helix.
Watching a molecule in solution is like watching a marionette- you can see it bending in response to making and breaking of hydrogen bonds,” said David Prendergast, a staff scientist in the Theory of Nanostructures Facility at the Molecular Foundry.
Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies.
The thickening mechanism has been explained as being caused by the formation of hydrogen bonds to carboxyl groups and water molecules, and structural viscosity owing to the three-dimensional network formed by the thickener polymer's adsorption to pigment particles.
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