Example sentences for: all-atom

How can you use “all-atom” in a sentence? Here are some example sentences to help you improve your vocabulary:

  • The scoring function for minimisation is primarily a combination of the all-atom function, a hydrophobic compactness function, and a bad contacts function [ 40 ] . The primary search technique we used was a Metropolis Monte Carlo (MC) procedure where conformations are accepted or rejected based on the Boltzmann's equation [ 41 ] . Each trajectory was allowed 50,000 iterations, starting with a high temperature such that 99% of the moves were accepted for the first 1000 steps and "cooled" linearly until only 1% of the moves were accepted for the last 100 steps.

  • We initially start with an all-atom conformation where the torsion values for residues predicted to be in helix/sheet by PSIPRED secondary structure prediction [ 38 ] are set to idealised values [ 33 ] . The remaining φ/ψ values are set in an extended conformation.

  • As shown in Table 1, the correlation coefficient significantly decreased from 0.87 at 0.1 ps to 0.74 at 10 ps as the all-atom flap RMSD increased from 0.54 to 3.30 at 0.1 and 10 ps, respectively.

  • MD simulation has been used to study the movement of the flap region of HIV-1 protease with a ligand [ 25 26 27 28 29 30 ] . The flaps initially opened to an all-atom RMSD of 25 Å within 200 ps and became completely open at the end of a 10 ns simulation.

  • The all-atom scoring function is the core of many aspects of this project where identification of native-like conformations is required.


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