Aleš Křenek

Jana Pazúriková, Jaroslav Oľha, Aleš Křenek et al.

Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing the~simulated process. However, the~evaluation of these variables can include numerous mean square distance calculations that introduce substantial computational demands, thus jeopardize the~benefit of the~approach. Recently, we proposed an~approximative method that significantly reduces the~number of these distance calculations. Here we evaluate the~performance and the~scalability on two molecular systems. We assess the~maximal theoretical speed-up based on the reduction of distance computations and Ahmdal's law and compare it to the~practical speed-up achieved with our implementation.

Adam Hájek, Michal Starý, Filip Jozefov et al.

Identification of experimentally acquired mass spectra of unknown compounds presents a~particular challenge because reliable spectral databases do not cover the potential chemical space with sufficient density. Therefore machine learning based \emph{de-novo} methods, which derive molecular structure directly from its mass spectrum gained attention recently. We present a~novel method in this family, addressing a~specific usecase of GC-EI-MS spectra, which is particularly hard due to lack of additional information from the first stage of MS/MS experiments, on which the previously published methods rely. We analyze strengths and drawbacks or our approach and discuss future directions.

Adam Hájek, Helge Hecht, Elliott J. Price et al.

Compound identification and structure annotation from mass spectra is a well-established task widely applied in drug detection, criminal forensics, small molecule biomarker discovery and chemical engineering. We propose SpecTUS: Spectral Translator for Unknown Structures, a deep neural model that addresses the task of structural annotation of small molecules from low-resolution gas chromatography electron ionization mass spectra (GC-EI-MS). Our model analyzes the spectra in \textit{de novo} manner -- a direct translation from the spectra into 2D-structural representation. Our approach is particularly useful for analyzing compounds unavailable in spectral libraries. In a rigorous evaluation of our model on the novel structure annotation task across different libraries, we outperformed standard database search techniques by a wide margin. On a held-out testing set, including \numprint{28267} spectra from the NIST database, we show that our model's single suggestion perfectly reconstructs 43\% of the subset's compounds. This single suggestion is strictly better than the candidate of the database hybrid search (common method among practitioners) in 76\% of cases. In a~still affordable scenario of~10 suggestions, perfect reconstruction is achieved in 65\%, and 84\% are better than the hybrid search.