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 high-throughput docking implemented in the ICM program [ 10 ] was applied.
We applied a flexible virtual screening algorithm (Molsoft ICM, virtual library screening module [ 17]) which rapidly docks hundreds of thousands of flexible compound structures into the ligand binding pocket of RAR, and discovered two novel RAR-β selective agonists.
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 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 sequences of AChBP, and of the alpha3, alpha4, alpha7, beta2 and beta4 nAChR monomers were aligned using the ICM multiple sequence alignment algorithm that includes the following steps [ 16 10 ] : 1) pairwise alignment using Needleman and Wunsch algorithm modified to use zero end gap penalties (so called ZEGA) [ 15 16 ] . 2) evolutionary tree construction with a "neighbor-joining algorithm" to determine the order of alignment and calculate relative weights of sequences and profiles from the branch lengths [ 17 ] . 3) traverse the tree from top to bottom, aligning the closest sequences or profiles.
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