Biological Physics and Bioinformatics Seminar
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2025-10-08 (Wednesday)
Audytorium, IFPAN, al. Lotników 32/46 at 15:15 
Dr Jer-Lai Kuo (Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan)Neural network-assisted first-principles exploration on the conformational space of peptides and saccharides
Link to the meeting: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
Sampling of the conformational space of peptides and saccharides with first-principle accuracy is critical as such a database provide a solid base to interpret experimental measurements such as Infrared photo-dissociation (IRPD) spectroscopy, ion mobility spectrometry (IMS), or collision-induced dissociation (CID). The conformational space of both peptides and saccharides are highly flexible, in which the distinct conformers of mono- and di-saccharide is estimated to be in the order of 103 and 106, respectively. To efficiently explore the diverse conformational space of saccharide without losing accuracy, we developed a multi-level sampling scheme integrating semi-empirical models, density function theory (DFT) and neural network potential (NNP) that can be routinely be applied to study di-saccharides and hexa-peptides. Preliminary results, shown on the right, demonstrate the decent agreement between experimental IRPD spectra and IR absorption simulated based on low-energy conformers of sodiated Gal-14GlcNAc at DFT. We are optimistic that the combination of theory and gas-phase experimental can provide a new dimension into explore the structures of these bio-molecules.