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.

  • Using the all-atom function alone to select native-like conformations is not likely to suffice when it is also used in the actual minimisation/search process, since all conformations generated in such searches represent local minima of this function.

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

  • Generally, the lowest binding energy clusters are associated with the lowest all-atom RMSDs of the ligands.

  • 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.

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