Words similar to all-atom

Example sentences for: all-atom

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Comparative modelling and fold recognition: Alignment and template selection using all-atom scoring functions
These structures also have low (≅ 0.3 Å) average all-atom root mean square deviations (RMSD) relative to the experimental results.
All models produced are refined using the Energy Calculation and Dynamics (ENCAD) package [ 36 ] . For a given protein sequence, there could be more than one all-atom model produced.
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 ] .
Generally, the lowest binding energy clusters are associated with the lowest all-atom RMSDs of the ligands.