Deciphering the RRM-RNA recognition code: A computational analysis.

Autor: Joel Roca-Martínez, Hrishikesh Dhondge, Michael Sattler, Wim F Vranken

Publikováno v: PLoS Computational Biology, Vol 19, Iss 1, p e1010859 (2023)

RNA recognition motifs (RRM) are the most prevalent class of RNA binding domains in eucaryotes. Their RNA binding preferences have been investigated for almost two decades, and even though some RRM domains are now very well described, their RNA recog

Externí odkaz: https://doaj.org/article/75592b152ec148f4a6f880096eab7b91

Challenges in describing the conformation and dynamics of proteins with ambiguous behavior

Autor: Joel Roca-Martinez, Tamas Lazar, Jose Gavalda-Garcia, David Bickel, Rita Pancsa, Bhawna Dixit, Konstantina Tzavella, Pathmanaban Ramasamy, Maite Sanchez-Fornaris, Isel Grau, Wim F. Vranken

Publikováno v: Frontiers in Molecular Biosciences, Vol 9 (2022)

Traditionally, our understanding of how proteins operate and how evolution shapes them is based on two main data sources: the overall protein fold and the protein amino acid sequence. However, a significant part of the proteome shows highly dynamic a

Externí odkaz: https://doaj.org/article/cb1cd7e3a07a4ee9b141fef663760725

Auto-encoding NMR chemical shifts from their native vector space to a residue-level biophysical index

Autor: Gabriele Orlando, Daniele Raimondi, Wim F. Vranken

Publikováno v: Nature Communications, Vol 10, Iss 1, Pp 1-9 (2019)

NMR chemical shift information is highly valuable in the investigation of small molecule and protein structure. Here, the authors developed a neural network approach to unify protein chemical shifts and their changes in response to changes in protein

Externí odkaz: https://doaj.org/article/61e9c1f7f5bf4e32be70987487f4bd26

Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins

Autor: Daniele Raimondi, Gabriele Orlando, Rita Pancsa, Taushif Khan, Wim F. Vranken

Publikováno v: Scientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)

Abstract Protein folding is a complex process that can lead to disease when it fails. Especially poorly understood are the very early stages of protein folding, which are likely defined by intrinsic local interactions between amino acids close to eac

Externí odkaz: https://doaj.org/article/f11ec48e3bdc45e38bd7fe3ddc31b01f

PDBe-KB: collaboratively defining the biological context of structural data

Autor: David Bednar, Sucharita Dey, Emmanuel D. Levy, Natarajan Kannan, Bissan Al-Lazikani, Damiano Piovesan, Luis A Rodriguez, Sameer Velankar, Mihaly Varadi, Jan Stourac, Jaime Prilusky, Manjeet Kumar, Radoslav Krivak, Michael J.E. Sternberg, Juan Fernandez Recio, Daniel Zaidman, David R. Armstrong, Nathan J Rollins, Gulzar Singh, Jiri Damborsky, Dandan Xue, Stephen Anyango, Vivek Modi, Antonio Rosato, Christine A. Orengo, Valeria Putignano, Radka Svobodová, Alessia David, Debora S. Marks, Roland L. Dunbrack, Jose Ramon Macias, David Jakubec, Mark N. Wass, Luis Serrano, Silvio C. E. Tosatto, John M. Berrisford, Ahsan Tanweer, Sreenath Nair, Geoffrey J. Barton, Wim F. Vranken, Lukáš Pravda, Karel Berka, Stuart A McGowan, Janet M. Thornton, Nir London, Madhusudhan M Srivatsan, Lennart Martens, Atilio O Rausch, Toby J. Gibson, Pawel Rubach, Joanna I. Sulkowska, Petr Škoda, Gerardo Pepe, Nathalie Reuter, Natalia Tichshenko, Mandar Deshpande, Franca Fraternali, David Hoksza, Tom L. Blundell, R. Gonzalo Parra, Preeti Choudhary, José María Carazo, Claudia Andreini, Jake E McGreig, Leandro G Radusky, Thomas A. Hopf, Pathmanaban Ramasamy, Carlos Oscar S. Sorzano, Manuela Helmer-Citterich, Kelly P Brock, Nurul Nadzirin

Publikováno v: Nucleic acids research
Nucleic Acids Research
Nucleic Acids Research (NAR)
D534-D542
UPCommons. Portal del coneixement obert de la UPC
Universitat Politècnica de Catalunya (UPC)
D542
D534

The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Dat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::050cb89e62952b78f542717c68240da1
https://kar.kent.ac.uk/95049/1/gkab988.pdf