Sentence examples for structural clashes from inspiring English sources

The dimeric models were minimized for 2000 steps to remove structural clashes using the conjugate gradient algorithm.

MolProbity[21], [22] clash scores for both the whole protein and individual residues were also compared to identify structural clashes resulting from the mutations.

Structural superimposition of LepB GAP domain with VirA-Rab1 or Gyp1p-Rab33 complex (see below), which places Arg444 in a position equivalent to that of the catalytic arginine in VirA/Gyp1p and amenable to interacting with GDP and AlFn, revealed no structural clashes but instead a well accommodation of Rab1/33 in the open space of the V-shaped valley.

Moreover, it helps to correct structural errors like steric clashes, misassigned side chain amides in glutamine and asparagine, and problematic rotamers.

Other uncertainties and controversies are difficult to handle today and bear the potentials of future clashes at various structural levels.

The structural model confirms the steric clashes predicted in the structural model built using an elongation complex structure, and reveals new, particularly severe, steric clashes involving the triphosphate of the first initiating NTP.

We have mutated each residue in the structure into the alternative amino acid, and the result was inspected site by site, verifying predictable structural alterations due to steric clashes and inspecting possible changes in polarity close to relevant protein regions such as proton channels and redox centers.

Unfortunately, that ambition sometimes clashed with the structural and cultural limits of the system in Ghana.

The resulting structural model predicts severe steric clash between GE and both the RNA 3′ nucleotide in the i site and the NTP in the i+1 site.

The resulting structural model shows severe steric clash between GE and both the first initiating NTP in the i site and the second initiating NTP in the i+1 site.

Keeping the initial orientation of structural elements could lead to atom clashes and bond crossings.