Words similar to icm
Example sentences for: icm
How can you use “icm” in a sentence? Here are some example sentences to help you improve your vocabulary:
The rotation variables of the side chains within 3.5 Å of the modified residues were unfixed and the energy of the system was minimized in the internal coordinate space, according to the ICM method [ 26, 29].
The ICM program [ 17] was used to perform both receptor modeling and virtual ligand screening.
The flexible ligand / grid receptor docking algorithm implemented in ICM was applied, with ECEPP/3 force field and MMFF partial charges for the ligand, and hydrophobic, electrostatic, hydrogen-bond and surface potential maps for the receptor [ 18 19 10 ] . Further optimization with flexible ligand and full atom representation of the receptor was carried out by local energy minimization, where all side-chains within 6 A of the ligand were flexible [ 18 ] . When docking was performed in the presence of a water molecule, the later was included in the grid representation of the receptor, and was mobile during full-atom local minimization.
The binding energy function implemented in icm is partitioned into three terms: the hydrophobic, or cavity term, that accounts for the variation of water/non-water interface area, the electrostatic term, composed of the coulombic interactions and desolvation of partial charges calculated by the boundary elements method, and the entropic term, that results from the decrease in the conformational freedom of functional groups buried upon complexation [ 20 ] . A constant term also present in the energy function, that accounts for the change of entropy of the system due to the decrease of free molecules concentration and the loss of rotational/translational degrees of freedom, was omitted, and only differences in the binding energies of the ligands are accurate.
The high-throughput docking implemented in the ICM program [ 10 ] was applied.
Loading...