Machine learning coarse-grained potentials of protein thermodynamics

Autor: Maciej Majewski, Adrià Pérez, Philipp Thölke, Stefan Doerr, Nicholas E. Charron, Toni Giorgino, Brooke E. Husic, Cecilia Clementi, Frank Noé, Gianni De Fabritiis

Publikováno v: Nature Communications, Vol 14, Iss 1, Pp 1-13 (2023)

Abstract A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach

Externí odkaz: https://doaj.org/article/7874019063c44680acebcb0eb6d2fbc6

Current Wildland Fire Patterns and Challenges in Europe: A Synthesis of National Perspectives

Autor: Nieves Fernandez-Anez, Andrey Krasovskiy, Mortimer Müller, Harald Vacik, Jan Baetens, Emira Hukić, Marijana Kapovic Solomun, Irena Atanassova, Maria Glushkova, Igor Bogunović, Hana Fajković, Hakan Djuma, George Boustras, Martin Adámek, Miloslav Devetter, Michaela Hrabalikova, Dalibor Huska, Petra Martínez Barroso, Magdalena Daria Vaverková, David Zumr, Kalev Jõgiste, Marek Metslaid, Kajar Koster, Egle Köster, Jukka Pumpanen, Caius Ribeiro-Kumara, Simone Di Prima, Amandine Pastor, Cornelia Rumpel, Manuel Seeger, Ioannis Daliakopoulos, Evangelia Daskalakou, Aristeidis Koutroulis, Maria P. Papadopoulou, Kosmas Stampoulidis, Gavriil Xanthopoulos, Réka Aszalós, Deák Balázs, Miklós Kertész, Orsolya Valkó, David C. Finger, Throstur Thorsteinsson, Jessica Till, Sofia Bajocco, Antonio Gelsomino, Antonio Minervino Amodio, Agata Novara, Luca Salvati, Luciano Telesca, Nadia Ursino, Aris Jansons, Mara Kitenberga, Normunds Stivrins, Gediminas Brazaitis, Vitas Marozas, Olesea Cojocaru, Iachim Gumeniuc, Victor Sfecla, Anton Imeson, Sander Veraverbeke, Ragni Fjellgaard Mikalsen, Eugeniusz Koda, Piotr Osinski, Ana C. Meira Castro, João Pedro Nunes, Duarte Oom, Diana Vieira, Teodor Rusu, Srđan Bojović, Dragana Djordjevic, Zorica Popovic, Milan Protic, Sanja Sakan, Jan Glasa, Danica Kacikova, Lubomir Lichner, Andrea Majlingova, Jaroslav Vido, Mateja Ferk, Jure Tičar, Matija Zorn, Vesna Zupanc, M. Belén Hinojosa, Heike Knicker, Manuel Esteban Lucas-Borja, Juli Pausas, Nuria Prat-Guitart, Xavier Ubeda, Lara Vilar, Georgia Destouni, Navid Ghajarnia, Zahra Kalantari, Samaneh Seifollahi-Aghmiuni, Turgay Dindaroglu, Tugrul Yakupoglu, Thomas Smith, Stefan Doerr, Artemi Cerda

Publikováno v: Air, Soil and Water Research, Vol 14 (2021)

Changes in climate, land use, and land management impact the occurrence and severity of wildland fires in many parts of the world. This is particularly evident in Europe, where ongoing changes in land use have strongly modified fire patterns over the

Externí odkaz: https://doaj.org/article/2dabc99510954ccba57f2317ffe81553

Evaluation of K-Ras4B dimer interfaces and the role of Raf effectors

Autor: Alexios Chatzigoulas, Ioannis Andreadelis, Stefan Doerr, Christos Lamprakis, Anastasia Theodoropoulou, John Manchester, Camilo Velez-Vega, Jose Duca, Zoe Cournia

K-Ras4B is one the most frequently mutated proteins in cancer, yet mechanistic details of its activation such as its homodimerization on the membrane remain elusive. The structural determinants of K-Ras4B homodimerization have been debated with diffe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::4f56b533fdd7dfaa074169030733f212
https://doi.org/10.1101/2022.10.04.510804

Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability

Autor: Anastasia Theodoropoulou, Camilo Velez-Vega, Ioannis Andreadelis, Zoe Cournia, Sofia Kiriakidi, José S. Duca, John I. Manchester, Christos Lamprakis, Stefan Doerr, Alexios Chatzigoulas

Ras proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the properties of Ras in terms of dimerization/clustering on the cell membrane. To unde

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::63841579a7ef7effee5d356e96d04aa8
https://doi.org/10.26434/chemrxiv-2021-4pdzb

AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations

Autor: Gianni De Fabritiis, Stefan Doerr, Adrià Pérez, Pablo Herrera-Nieto

Publikováno v: Journal of chemical theory and computation. 16(7)

Sampling from the equilibrium distribution has always been a major problem in molecular simulations due to the very high dimensionality of the conformational space. Over several decades, many approaches have been used to overcome the problem. In part

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a8b195c011b212dae4146459473f47b1
https://pubmed.ncbi.nlm.nih.gov/32539384