Fully Automatable Relative Binding Free Energy Calculations with Enhanced Sampling Using FAST/MBAR
Miroslav Suruzhon, Justina Ratkeviciute, Khaled Abdel-Maksoud, Anna Cavalleri, Michael S. Bodnarchuk, Antonella Ciancetta, Ian D. Wall, Jonathan W. Essex · 2026
Read Fully Automatable Relative Binding Free Energy Calculations with Enhanced Sampling Using FAST/MBAR by Miroslav Suruzhon, Justina Ratkeviciute, Khaled Abdel-Maksoud, Anna Cavalleri, Michael S. Bodnarchuk, Antonella Ciancetta, Ian D. Wall, Jonathan W. Essex (2026) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/PMC13472099.txt.
Description
Suruzhon and colleagues extended a computing method in 2026 for ranking how strongly drug-like molecules bind to their targets. Alchemical free energy calculations, which slowly morph one molecule into another, help drug hunters rank candidates, but short runs make results depend heavily on the starting shape of the system. The team's FAST method adjusts simulation heat on the fly to sample more widely.
Coupling FAST with the MBAR estimator, a way to combine many simulation states, gave two modes: one that pushes sampling of a chosen twisting motion, and one that leaves the system free. Pushing the chosen motion sped its movement but spread sampling more thinly elsewhere. Free runs kept some starting-shape bias yet still captured slow twisting events within billionths of a second. Because the setup is fully automatic, the authors present it as a robust rival to standard methods for drug ranking work.
Catalog record
| CREATOR | Miroslav Suruzhon, Justina Ratkeviciute, Khaled Abdel-Maksoud, Anna Cavalleri, Michael S. Bodnarchuk, Antonella Ciancetta, Ian D. Wall, Jonathan W. Essex |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 63 KB |
| LICENSE | https://creativecommons.org/licenses/by/4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |