Overlay databank unlocks data-driven analyses of biomolecules for all

Autor: Anne M. Kiirikki, Hanne S. Antila, Lara S. Bort, Pavel Buslaev, Fernando Favela-Rosales, Tiago Mendes Ferreira, Patrick F. J. Fuchs, Rebeca Garcia-Fandino, Ivan Gushchin, Batuhan Kav, Norbert Kučerka, Patrik Kula, Milla Kurki, Alexander Kuzmin, Anusha Lalitha, Fabio Lolicato, Jesper J. Madsen, Markus S. Miettinen, Cedric Mingham, Luca Monticelli, Ricky Nencini, Alexey M. Nesterenko, Thomas J. Piggot, Ángel Piñeiro, Nathalie Reuter, Suman Samantray, Fabián Suárez-Lestón, Reza Talandashti, O. H. Samuli Ollila

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-15 (2024)

Abstract Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solutio

Externí odkaz: https://doaj.org/article/acfa193917a24cbab8ffde269f7d7c0d

Abstract P-2: Modeling Encapsulated Lipid Molecules in Cryo-EM Maps of Membrane Complexes

Autor: Olga Novitskaia, Pavel Buslaev, Ivan Gushchin

Publikováno v: International Journal of Biomedicine, Vol 9, Iss Suppl_1, Pp S17-S17 (2019)

Background: Membrane complexes are of great importance for cell functioning. Among the best studied complexes are rotor ATPases which create ATP from ADP, or vice versa (J.E. Walker, Biochem. Soc. Trans. 41, pp. 1-16, 2013). Generally, rotor ATPases

Externí odkaz: https://doaj.org/article/81cd3b7924d24226bc360b59c2b7f338

gmXtal: Cooking crystals with GROMACS

Autor: Pavel Buslaev, Gerrit Groenhof

Molecular dynamics (MD) simulations are routinely performed of biomolecules in solution, because this is their native environment. However, the structures used in such simulations are often obtained with x-ray crystallography, which provides the atom

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::d01d646d047614029c992fa968e2e65c
https://doi.org/10.21203/rs.3.rs-2894952/v1

Inverse Conformational Selection in Lipid–Protein Binding

Autor: Matti Javanainen, Salla I. Virtanen, Fernando Favela-Rosales, Chris Papadopoulos, Antonio Peón, Amélie Bacle, Anne M. Kiirikki, Patrick F.J. Fuchs, O. H. Samuli Ollila, Pavel Buslaev, Ángel Piñeiro, Rebeca García-Fandiño, Paula Milán Rodríguez, Tiago Mendes Ferreira, Markus S. Miettinen, Jesper J. Madsen, Josef Melcr, Ivan Gushchin, Thomas J. Piggot

Publikováno v: Journal of the American Chemical Society
Journal of the American Chemical Society, 2021, 143 (34), pp.13701-13709. ⟨10.1021/jacs.1c05549⟩
Journal of the American Chemical Society, 143(34), 13701-13709. AMER CHEMICAL SOC
Journal of the American Chemical Society, American Chemical Society, 2021, 143 (34), pp.13701-13709. ⟨10.1021/jacs.1c05549⟩

International audience; Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology where lipids are commonly used, for example, in carriers of mRNA v

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c2d9345531ed2d3d157ba5bfda9d2f8b
https://hal.sorbonne-universite.fr/hal-03355166/file/jacs.1c05549.pdf

A thermostable flavin-based fluorescent protein from Chloroflexus aggregans: a framework for ultra-high resolution structural studies

Autor: Ivan M. Goncharov, Pavel Kuzmichev, Karl-Erich Jaeger, Gaurao V. Dhoke, Ivan Gushchin, Valentin Gordeliy, Valentin Borshchevskiy, Anton Dubenko, Pavel Buslaev, Alina Remeeva, A. V. Rogachev, Mehdi D. Davari, Ulrich Schwaneberg, Anna Yudenko, Ulrich Krauss, Vera V. Nazarenko, Kirill Kovalev, Alexey Mishin

Publikováno v: Photochemical & photobiological sciences 18(7), 1793-1805 (2019). doi:10.1039/C9PP00067D

Light-Oxygen-Voltage (LOV) domains are conserved parts of photoreceptors in plants, bacteria and fungi that bind flavins as chromophores and detect blue light. In the past, LOV domain variants have been developed as fluorescent reporter proteins (cal

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::963630be4375f5a4b807f4e561e55f0d
https://doi.org/10.1039/c9pp00067d