Words similar to all-atom
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:
Generally, the lowest binding energy clusters are associated with the lowest all-atom RMSDs of the ligands.
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.
Even though our all-atom function is readily able to distinguish native-like conformations in certain scenarios, it is not adequate for large sets of decoys where the closest conformation generated is represented at the topological level (≈ 6.0 Å C α RMSD relative to the experimental result).
Docking solutions with ligand all-atom RMSDs within 1.0 Å of each other were clustered together and ranked by the lowest energy representative.
The scoring functions used for the final filtering include the all-atom function [ 32 ] , hydrophobic compactness [ 40 ] , a simple residue-residue contact function [ 44 ] , a density-scoring function that is based on the distance of a conformation to all its relatives in the conformation pool, contact order [ 45 ] , a secondary structure based scoring function that evaluates the match between the predicted structure and the secondary structure of a final energy-minimised conformation, and standard physics-based electrostatics and Van der Waals terms [ 46 ] .
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