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 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.
The high-throughput docking implemented in the ICM program [ 10 ] was applied.
This rapid docking procedure was followed by a more refined energy minimization of the complex, with a full atom representation of the receptor, and flexible receptor side chains, according to the ICM stochastic global optimization algorithm [ 26, 27] as implemented in the Molsoft ICM 2.7 program [ 17].
The ICM program [ 17] was used to perform both receptor modeling and virtual ligand screening.
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.
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