{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kearns FL"],"funding":["Austrian Science Fund FWF","National Institutes of Health","NIGMS NIH HHS","NIH HHS","National Science Foundation"],"pagination":["E681"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC6413162"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["24(4)"],"pubmed_abstract":["Indirect (S)QM/MM free energy simulations (FES) are vital to efficiently incorporating sufficient sampling and accurate (QM) energetic evaluations when estimating free energies of practical/experimental interest. Connecting between levels of theory, i.e., calculating Δ A l o w → h i g h , remains to be the most challenging step within an indirect FES protocol. To improve calculations of Δ A l o w → h i g h , we must: (1) compare the performance of all FES methods currently available; and (2) compile and maintain datasets of Δ A l o w → h i g h calculated for a wide-variety of molecules so that future practitioners may replicate or improve upon the current state-of-the-art. Towards these two aims, we introduce a new dataset, \"HiPen\", which tabulates Δ A g a s M M → 3 o b (the free energy as"],"journal":["Molecules (Basel, Switzerland)"],"pubmed_title":["The Good, the Bad, and the Ugly: \"HiPen\", a New Dataset for Validating (S)QM/MM Free Energy Simulations."],"pmcid":["PMC6413162"],"funding_grant_id":["MRI-1531590","3900101301","R01GM129519","CHE-1464946","P 31024","R01 GM129519","P31024"],"pubmed_authors":["Boresch S","Warrensford L","Woodcock HL","Kearns FL"],"additional_accession":[]},"is_claimable":false,"name":"The Good, the Bad, and the Ugly: \"HiPen\", a New Dataset for Validating (S)QM/MM Free Energy Simulations.","description":"Indirect (S)QM/MM free energy simulations (FES) are vital to efficiently incorporating sufficient sampling and accurate (QM) energetic evaluations when estimating free energies of practical/experimental interest. Connecting between levels of theory, i.e., calculating Δ A l o w → h i g h , remains to be the most challenging step within an indirect FES protocol. To improve calculations of Δ A l o w → h i g h , we must: (1) compare the performance of all FES methods currently available; and (2) compile and maintain datasets of Δ A l o w → h i g h calculated for a wide-variety of molecules so that future practitioners may replicate or improve upon the current state-of-the-art. Towards these two aims, we introduce a new dataset, \"HiPen\", which tabulates Δ A g a s M M → 3 o b (the free energy as","dates":{"release":"2019-01-01T00:00:00Z","publication":"2019 Feb","modification":"2026-04-08T00:16:35.442Z","creation":"2019-06-06T20:59:12Z"},"accession":"S-EPMC6413162","cross_references":{"pubmed":["30769826"],"doi":["10.3390/molecules24040681"]}}