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10.1007/s00706-016-1674-1 http://scihub22266oqcxt.onion/10.1007/s00706-016-1674-1 C4785218!4785218 !27069282     free     free     free Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=27069282 &cmd=llinks): Failed to open stream: HTTP request failed! 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Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations |pdf=|usr=}}{{27069282 }} gab.com Text Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations JO: Monatsh Chem http://www.kidney.de/pget.php?&tw=1&pmid=27069282 #FOAvip ABSTRACT: Pharmacophore modeling is a widely used technique in computer-aided drug discovery. Structure-based pharmacophore models of a ligand in complex with a protein have proven to be useful for supporting in silico hit discovery, hit to lead expansion, and lead optimization. As a structure-based approach it depends on the correct interpretation of ligand-protein interactions. There are legitimate concerns about the fidelity of the bound ligand and about non-physiological contacts with parts of the crystal and the solvent effects that influence the protein structure. A possible way to refine the structure of a protein-ligand system is to use the final structure of a given MD simulation. In this study we compare pharmacophore models built using the initial protein-ligand structure obtained from the protein data bank (PDB) with pharmacophore models built with the final structure of a molecular dynamics simulation. We show that the pharmacophore models differ in feature number and feature type and that the pharmacophore models built from the last structure of a MD simulation shows in some cases better ability to distinguish between active and decoy ligand structures. Twit Text FOAVip Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations ????Monatsh Chem http://www.kidney.de/pget.php?&tw=1&pmid=27069282 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=27069282 #FOAvip English Wikipedia <ref>{{Cite pmid|27069282 }}</ref> Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations #MMPMID27069282 Wieder M ; Perricone U ; Seidel T ; Boresch S ; Langer T Monatsh Chem 2016[]; 147 (ä): 553-563 PMID27069282 show ga ABSTRACT: Pharmacophore modeling is a widely used technique in computer-aided drug discovery. Structure-based pharmacophore models of a ligand in complex with a protein have proven to be useful for supporting in silico hit discovery, hit to lead expansion, and lead optimization. As a structure-based approach it depends on the correct interpretation of ligand-protein interactions. There are legitimate concerns about the fidelity of the bound ligand and about non-physiological contacts with parts of the crystal and the solvent effects that influence the protein structure. A possible way to refine the structure of a protein-ligand system is to use the final structure of a given MD simulation. In this study we compare pharmacophore models built using the initial protein-ligand structure obtained from the protein data bank (PDB) with pharmacophore models built with the final structure of a molecular dynamics simulation. We show that the pharmacophore models differ in feature number and feature type and that the pharmacophore models built from the last structure of a MD simulation shows in some cases better ability to distinguish between active and decoy ligand structures. äComparing pharmacophore models derived from crystal structures and fro(epmc).pdf DeepDyve Pubget Overpricing