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Binding studies are ubiquitous in chemistry, but their extensive usefulness is undermined by false positive and false negative results. Centering on the G-protein mini-Gs, we present a thorough study with both simulated and experimental spectrophotometric titration data to diagnose the validity of both binding and non-binding models. Without the use of statistical tests like Bayesian Information Criterion (BIC) and data reconstruction fractions, spurious binding models may go undetected. Furthermore, if the signal change upon binding is too minute, false negatives can also result. Delineating such issues is paramount to effective science.more » « lessFree, publicly-accessible full text available December 23, 2025
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Tribello, Gareth A; Bonomi, Massimiliano; Bussi, Giovanni; Camilloni, Carlo; Armstrong, Blake I; Arsiccio, Andrea; Aureli, Simone; Ballabio, Federico; Bernetti, Mattia; Bonati, Luigi; et al (, The Journal of Chemical Physics)In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software’s functionalities. To address these issues, here we introduce “PLUMED Tutorials,” a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources.more » « lessFree, publicly-accessible full text available March 7, 2026
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Amaro, Rommie E; Åqvist, Johan; Bahar, Ivet; Battistini, Federica; Bellaiche, Adam; Beltran, Daniel; Biggin, Philip C; Bonomi, Massimiliano; Bowman, Gregory R; Bryce, Richard A; et al (, Nature Methods)In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm.more » « lessFree, publicly-accessible full text available April 1, 2026
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