The development of target-specific pose filter ensembles to boost ligand enrichment for structure-based virtual screening
… on which FRED failed to generate docking poses because of … pose classifiers (ie, PFs),
106 were optimal models for pose prediction, whose values of both CV accuracy and prediction …
106 were optimal models for pose prediction, whose values of both CV accuracy and prediction …
Protein-Based Virtual Screening Tools Applied for RNA–Ligand Docking Identify New Binders of the preQ1-Riboswitch
E Kallert, TR Fischer, S Schneider… - Journal of Chemical …, 2022 - ACS Publications
… FlexX, FRED, and HYBRID were selected for a prospective VS against the Bacillus subtilis
preQ 1 -RS. All three programs showed high accuracy in binding mode prediction with re-…
preQ 1 -RS. All three programs showed high accuracy in binding mode prediction with re-…
High-throughput virtual screening and validation of a SARS-CoV-2 main protease noncovalent inhibitor
… When ligand-binding information was available in the receptor, HYBRID was used due to
its increased pose prediction accuracy over FRED. (19) HYBRID and FRED have the same …
its increased pose prediction accuracy over FRED. (19) HYBRID and FRED have the same …
Machine learning consensus scoring improves performance across targets in structure-based virtual screening
… A compound docked by FRED, for example, may not result in … The preferred solution
would be separate pose prediction … We find that ranking by MVC gains enrichment accuracy …
would be separate pose prediction … We find that ranking by MVC gains enrichment accuracy …
The discovery of novel HDAC3 inhibitors via virtual screening and in vitro bioassay
… , we selected top-ranking compounds from the lists of FRED and Vina, respectively. … , and
it was able to classify poses in a CV accuracy of 86.75% and a prediction accuracy of 87%. We …
it was able to classify poses in a CV accuracy of 86.75% and a prediction accuracy of 87%. We …
The use of fake ligands from computational solvent mapping in ligand and structure-based virtual screening
DR Hall, IJ Enyedy - Future Medicinal Chemistry, 2016 - Taylor & Francis
… of computational solvent mapping with virtual screening was performed with FRED. This …
the ligand to a better pose and more accurately distinguish active from inactive molecules. …
the ligand to a better pose and more accurately distinguish active from inactive molecules. …
Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking
… In the Procedure, we outline the steps to prepare grids for docking with Glide or FRED. … ,
reporting sample size, test set recall value, test set precision and predicted number of remaining …
reporting sample size, test set recall value, test set precision and predicted number of remaining …
Pose filter-based ensemble learning enables discovery of orally active, nonsteroidal farnesoid x receptor agonists
J Xia, Z Wang, Y Huan, W Xue, X Wang… - Journal of chemical …, 2020 - ACS Publications
… Unfortunately, structure-based virtual screening (SBVS) that … a prediction accuracy (PA)
value of 92.49% and the poses of … of 3RUT by FRED, with only the top-scoring pose retained for …
value of 92.49% and the poses of … of 3RUT by FRED, with only the top-scoring pose retained for …
Fragment pose prediction using non-equilibrium candidate Monte Carlo and molecular dynamics simulations
… -protein structure using FRED from OEDock (v3.2.0.2), generating 1000 docked poses, and
… given the force fields, protonation states, accuracy of our model, and simulation timescales …
… given the force fields, protonation states, accuracy of our model, and simulation timescales …
Machine learning classification can reduce false positives in structure-based virtual screening
YO Adeshina, EJ Deeds… - Proceedings of the …, 2020 - National Acad Sciences
… as the popular FRED Chemgauss4 scoring function (64). … We took for each method the
top five predicted activities for … We then calculated accuracy, precision, recall, area under …
top five predicted activities for … We then calculated accuracy, precision, recall, area under …