PROPTIMUS LIVE: local constrained α-carbon optimization of proteins

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Authors	SVOBODA Tomáš MIKUŠ Michal BOHUŠ Lukáš RAČEK Tomáš BUČEKOVÁ Gabriela TICHÝ Dominik BERKA Karel SVOBODOVÁ Radka SCHINDLER Ondřej
Year of publication	2026
Type	Peer-reviewed scientific article
Magazine / Source	Nucleic Acids Research
MU Faculty or unit	Faculty of Science
Citation
web	https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag511/8687947
Doi	https://doi.org/10.1093/nar/gkag511
Description	High-quality protein structures are essential for a wide range of computational chemistry applications. While experimental methods and predictive algorithms provide high-accuracy positions of protein residues relative to one another, the local quality of these structures, including bond lengths, angles, and individual atom positions, often lacks the same level of precision. To address this, we developed PROPTIMUS LIVE, a web application offering local constrained ?-carbon optimization of protein structures. PROPTIMUS LIVE is powered by the QM-accurate, physics-based GFN-Force-Field and accelerated using a divide-and-conquer approach, allowing typical optimizations to finish within minutes. Optimized structures can be visualized and investigated directly via the integrated Mol* Viewer. The service is freely available at https://proptimus.ceitec.cz/live with no login required, including for commercial use.