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Enhanced Sampling with Machine Learning.
Mehdi S, Smith Z, Herron L, Zou Z, Tiwary P. Mehdi S, et al. Annu Rev Phys Chem. 2024 Jun;75(1):347-370. doi: 10.1146/annurev-physchem-083122-125941. Epub 2024 Jun 14. Annu Rev Phys Chem. 2024. PMID: 38382572 Free PMC article. Review.
PLUMED Tutorials: A collaborative, community-driven learning ecosystem.
Tribello GA, Bonomi M, Bussi G, Camilloni C, Armstrong BI, Arsiccio A, Aureli S, Ballabio F, Bernetti M, Bonati L, Brookes SGH, Brotzakis ZF, Capelli R, Ceriotti M, Chan KT, Cossio P, Dasetty S, Donadio D, Ensing B, Ferguson AL, Fraux G, Gale JD, Gervasio FL, Giorgino T, Herringer NSM, Hocky GM, Hoff SE, Invernizzi M, Languin-Cattoën O, Leone V, Limongelli V, Lopez-Acevedo O, Marinelli F, Febrer Martinez P, Masetti M, Mehdi S, Michaelides A, Murtada MH, Parrinello M, Piaggi PM, Pietropaolo A, Pietrucci F, Pipolo S, Pritchard C, Raiteri P, Raniolo S, Rapetti D, Rizzi V, Rydzewski J, Salvalaglio M, Schran C, Seal A, Shayesteh Zadeh A, Silva TFD, Spiwok V, Stirnemann G, Sucerquia D, Tiwary P, Valsson O, Vendruscolo M, Voth GA, White AD, Wu J. Tribello GA, et al. Among authors: mehdi s. J Chem Phys. 2025 Mar 7;162(9):092501. doi: 10.1063/5.0251501. J Chem Phys. 2025. PMID: 40035582 Free article.
Machine learning-augmented molecular dynamics simulations (MD) reveal insights into the disconnect between affinity and activation of ZTP riboswitch ligands.
Fullenkamp CR, Mehdi S, Jones CP, Tenney L, Pichling P, Prestwood PR, Ferré-D'Amaré AR, Tiwary P, Schneekloth JS Jr. Fullenkamp CR, et al. Among authors: mehdi s. bioRxiv [Preprint]. 2024 Sep 14:2024.09.13.612887. doi: 10.1101/2024.09.13.612887. bioRxiv. 2024. Update in: Angew Chem Int Ed Engl. 2025 May 1:e202505971. doi: 10.1002/anie.202505971. PMID: 39314358 Free PMC article. Updated. Preprint.
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