April 2024 - Bioinf-l - kam.mff.cuni.cz

Lecture invitation: Semiempirical Quantum Mechanical Scoring in Structure-based Drug Design
by Petr Danecek 23 Apr '24

23 Apr '24

Dear all, the next seminar will take place on Wednesday *(tomorrow!)*, please see the details below. We look forward to seeing you all! Title: Semiempirical Quantum Mechanical Scoring in Structure-based Drug Design Speaker: Jan Řezáč (UOCHB AVCR) Date and time: Wednesday 24.4.2024 - 17:20 Location: MFF UK, Malostranské nám. 25, lecture hall S4 (3rd floor) https://bioinformatics.cuni.cz/seminar/ Best wishes, Petr Danecek

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Lecture invitation: From human population variation to ligand binding sites via SARS-CoV-2
by Petr Danecek 15 Apr '24

15 Apr '24

Dear all, the next seminar will take place on Wednesday, please see the details below. We look forward to seeing you all! Title: From human population variation to ligand binding sites via SARS-CoV-2 Speaker: Geoff Barton (University of Dundee) Date and time: Wednesday 17/04/2024 - 17:20 Location: MFF UK, Malostranské nám. 25, lecture hall S4 https://bioinformatics.cuni.cz/seminar/ Best wishes, Petr Danecek ------------------------------- *Geoff Barton (University of Dundee)* */From human population variation to ligand binding sites via SARS-CoV-2 /* In this talk I will present an analysis that compares publicly available variation data for human with variation seen across all available protein sequences regardless of species. The analysis confirms patterns of variation in human are consistent with protein structural features (e.g. alpha-helix and begta-strand) but highlights structurally and functionally important sites in around 15,000 human protein domains that are not found by conventional sequence analysis methods. The identified sites are enriched in disease-associated variants, ligand binding residues and protein-protein interaction sites. I will explain the method and illustrate the new analysis with examples including the Nuclear Receptor Ligand Binding Domains and G-protein coupled receptors (GPCRs) which are important therapeutic targets. The study makes heavy use of the popular Jalview (www.jalview.org) sequence analysis program developed since 1996 in my group, so I will also give a brief update on Jalview’s new features for exploring nsSNPs on alignments and three-dimensional structures including predictions by AlphaFold.

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Lecture invitation: Computational methods for prosthetic vision
by Petr Danecek 08 Apr '24

08 Apr '24

Dear all, the next seminar will take place on Wednesday, please see the details below. We look forward to seeing you all! Title: Computational methods for prosthetic vision: inferring functional structure of the brain from its spontaneous activity Speaker: Karolína Korvasová (Charles University, Faculty of Mathematics and Physics) Date and time: Wednesday 10/04/2024 - 17:20 Location: MFF UK, Malostranské nám. 25, lecture hall S4 https://bioinformatics.cuni.cz/seminar/ Best wishes, Petr Danecek ------------------------------- * Karolína Korvasová* (Charles University, Faculty of Mathematics and Physics) */Computational methods for prosthetic vision: inferring functional structure of the brain from its spontaneous activity/* Being able to infer the functional structure of cortical neural networks from their spontaneous activity would advance our understanding of neural dynamics and have important applications in the field of visual prosthetics, as functional properties of neurons in the visual cortex cannot be measured directly in blind subjects. We designed a method that estimates the structure of the orientation preference map in the primary visual cortex. Using this method, we were able to show that functional, as well as spatial properties of the sites stimulated with a cortical visual prosthesis in blind humans determine the perceptual outcome. In this talk I will first introduce some basic concepts of computational neuroscience and discuss how biological neural networks can be modeled. Next, I will briefly present a large-scale model of the primary visual cortex developed in the group of Ján Antolík (MFF UK) that was used to design the method that infers functional structure from spontaneous activity. Finally, I will show the results of this method applied to electrophysiological recordings from the visual cortex of sighted non-human primates and blind human volunteers.

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