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10.1007/s10822-020-00345-7 http://scihub22266oqcxt.onion/10.1007/s10822-020-00345-7 33034007!7544562!33034007     free     free     free Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=33034007&cmd=llinks): Failed to open stream: HTTP request failed! 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Combining fragment docking with graph theory to improve ligand docking for homology model structures |pdf=|usr=}}{{33034007}} gab.com Text Combining fragment docking with graph theory to improve ligand docking for homology model structures JO: J Comput Aided Mol Des http://www.kidney.de/pget.php?&tw=1&pmid=33034007 #FOAvip Computational protein-ligand docking is well-known to be prone to inaccuracies in input receptor structures, and it is challenging to obtain good docking results with computationally predicted receptor structures (e.g. through homology modeling). Here we introduce a fragment-based docking method and test if it reduces requirements on the accuracy of an input receptor structures relative to non-fragment docking approaches. In this method, small rigid fragments are docked first using AutoDock Vina to generate a large number of favorably docked poses spanning the receptor binding pocket. Then a graph theory maximum clique algorithm is applied to find combined sets of docked poses of different fragment types onto which the complete ligand can be properly aligned. On the basis of these alignments, possible binding poses of complete ligand are determined. This docking method is first tested for bound docking on a series of Cytochrome P450 (CYP450) enzyme-substrate complexes, in which experimentally determined receptor structures are used. For all complexes tested, ligand poses of less than 1 A root mean square deviations (RMSD) from the actual binding positions can be recovered. Then the method is tested for unbound docking with modeled receptor structures for a number of protein-ligand complexes from different families including the very recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protease. For all complexes, poses with RMSD less than 3 A from actual binding positions can be recovered. Our results suggest that for docking with approximately modeled receptor structures, fragment-based methods can be more effective than common complete ligand docking approaches. Twit Text FOAVip Combining fragment docking with graph theory to improve ligand docking for homology model structures ????J Comput Aided Mol Des http://www.kidney.de/pget.php?&tw=1&pmid=33034007 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=33034007 #FOAvip English Wikipedia <ref>{{Cite pmid|33034007}}</ref> Combining fragment docking with graph theory to improve ligand docking for homology model structures #MMPMID33034007 Sarfaraz S; Muneer I; Liu H J Comput Aided Mol Des 2020[Dec]; 34 (12): 1237-1259 PMID33034007show ga Computational protein-ligand docking is well-known to be prone to inaccuracies in input receptor structures, and it is challenging to obtain good docking results with computationally predicted receptor structures (e.g. through homology modeling). Here we introduce a fragment-based docking method and test if it reduces requirements on the accuracy of an input receptor structures relative to non-fragment docking approaches. In this method, small rigid fragments are docked first using AutoDock Vina to generate a large number of favorably docked poses spanning the receptor binding pocket. Then a graph theory maximum clique algorithm is applied to find combined sets of docked poses of different fragment types onto which the complete ligand can be properly aligned. On the basis of these alignments, possible binding poses of complete ligand are determined. This docking method is first tested for bound docking on a series of Cytochrome P450 (CYP450) enzyme-substrate complexes, in which experimentally determined receptor structures are used. For all complexes tested, ligand poses of less than 1 A root mean square deviations (RMSD) from the actual binding positions can be recovered. Then the method is tested for unbound docking with modeled receptor structures for a number of protein-ligand complexes from different families including the very recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protease. For all complexes, poses with RMSD less than 3 A from actual binding positions can be recovered. Our results suggest that for docking with approximately modeled receptor structures, fragment-based methods can be more effective than common complete ligand docking approaches. |*Molecular Docking Simulation[MESH] |*Pandemics[MESH] |ATPases Associated with Diverse Cellular Activities/chemistry/metabolism[MESH] |Betacoronavirus/*enzymology[MESH] |COVID-19[MESH] |Coronavirus 3C Proteases[MESH] |Coronavirus Infections/*drug therapy[MESH] |Cysteine Endopeptidases/chemistry/*drug effects/metabolism[MESH] |Cytochrome P-450 Enzyme System/chemistry/metabolism[MESH] |DNA-Binding Proteins/chemistry/metabolism[MESH] |Humans[MESH] |Ligands[MESH] |Models, Chemical[MESH] |Models, Molecular[MESH] |Molecular Chaperones/chemistry/metabolism[MESH] |Peptide Fragments/chemistry/metabolism[MESH] |Pneumonia, Viral/*drug therapy[MESH] |Protein Binding[MESH] |Protein Conformation[MESH] |Receptors, G-Protein-Coupled/chemistry/metabolism[MESH] |SARS-CoV-2[MESH] |Transcription Factors/chemistry/metabolism[MESH]Combining fragment docking with graph theory to improve ligand docking(epmc).pdf DeepDyve Pubget Overpricing