Graves, Alan P. published the artcileRescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing, Related Products of ethers-buliding-blocks, the main research area is protein ligand docking mol mechanics generalized Born surface area; virtual screening rescoring ligand crystal structure protein conformation.
Mol. docking computationally screens thousands to millions of organic mols. against protein structures, looking for those with complementary fits. Many approximations are made, often resulting in low “”hit rates.””. A strategy to overcome these approximations is to rescore top-ranked docked mols. using a better but slower method. One such is afforded by mol. mechanics-generalized Born surface area (MM-GBSA) techniques. These more phys. realistic methods have improved models for solvation and electrostatic interactions and conformational change compared to most docking programs. To investigate MM-GBSA rescoring, the authors reranked docking hit lists in three small buried sites: a hydrophobic cavity that binds apolar ligands, a slightly polar cavity that binds aryl and hydrogen-bonding ligands, and an anionic cavity that binds cationic ligands. These sites are simple; consequently, incorrect predictions can be attributed to particular errors in the method, and many likely ligands may actually be tested. In retrospective calculations, MM-GBSA techniques with binding-site minimization better distinguished the known ligands for each cavity from the known decoys compared to the docking calculation alone. This encouraged us to test rescoring prospectively on mols. that ranked poorly by docking but that ranked well when rescored by MM-GBSA. A total of 33 mols. highly ranked by MM-GBSA for the three cavities were tested exptl. Of these, 23 were observed to bind-these are docking false negatives rescued by rescoring. The 10 remaining mols. are true negatives by docking and false positives by MM-GBSA. X-ray crystal structures were determined for 21 of these 23 mols. In many cases, the geometry prediction by MM-GBSA improved the initial docking pose and more closely resembled the crystallog. result; yet in several cases, the rescored geometry failed to capture large conformational changes in the protein. Intriguingly, rescoring not only rescued docking false positives, but also introduced several new false positives into the top-ranking mols. The authors consider the origins of the successes and failures in MM-GBSA rescoring in these model cavity sites and the prospects for rescoring in biol. relevant targets.
Journal of Molecular Biology published new progress about Algorithm. 622-86-6 belongs to class ethers-buliding-blocks, name is (2-Chloroethoxy)benzene, and the molecular formula is C8H9ClO, Related Products of ethers-buliding-blocks.
Referemce:
Ether – Wikipedia,
Ether | (C2H5)2O – PubChem