Zobrazeno 1 - 10
of 16
pro vyhledávání: '"Vaitea Opuu"'
Publikováno v:
PLoS Computational Biology, Vol 18, Iss 8, p e1010448 (2022)
We propose a novel heuristic to predict RNA secondary structure formation pathways that has two components: (i) a folding algorithm and (ii) a kinetic ansatz. This heuristic is inspired by the kinetic partitioning mechanism, by which molecules follow
Externí odkaz:
https://doaj.org/article/3b97928a48754871a3a5e0d0ad41a80d
Autor:
Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Mechulam, Thomas Simonson
Publikováno v:
PLoS Computational Biology, Vol 16, Iss 1, p e1007600 (2020)
Designed enzymes are of fundamental and technological interest. Experimental directed evolution still has significant limitations, and computational approaches are a complementary route. A designed enzyme should satisfy multiple criteria: stability,
Externí odkaz:
https://doaj.org/article/a75e57bfe52c4f3cb75bf85829927450
Autor:
Nika Abdollahi, Alexandre Albani, Eric Anthony, Agnes Baud, Mélissa Cardon, Robert Clerc, Dariusz Czernecki, Romain Conte, Laurent David, Agathe Delaune, Samia Djerroud, Pauline Fourgoux, Nadège Guiglielmoni, Jeanne Laurentie, Nathalie Lehmann, Camille Lochard, Rémi Montagne, Vasiliki Myrodia, Vaitea Opuu, Elise Parey, Lélia Polit, Sylvain Privé, Chloé Quignot, Maria Ruiz-Cuevas, Mariam Sissoko, Nicolas Sompairac, Audrey Vallerix, Violaine Verrecchia, Marc Delarue, Raphael Guérois, Yann Ponty, Sophie Sacquin-Mora, Alessandra Carbone, Christine Froidevaux, Stéphane Le Crom, Olivier Lespinet, Martin Weigt, Samer Abboud, Juliana Bernardes, Guillaume Bouvier, Chloé Dequeker, Arnaud Ferré, Patrick Fuchs, Gaëlle Lelandais, Pierre Poulain, Hugues Richard, Hugo Schweke, Elodie Laine, Anne Lopes
Publikováno v:
PLoS Computational Biology, Vol 14, Iss 3, p e1005992 (2018)
We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and tak
Externí odkaz:
https://doaj.org/article/e780d76873364d1588f1c361ea6d3e72
Autor:
Kuang-Yu Chen, Jayaprakash Karuppusamy, Mary B. O’Neill, Vaitea Opuu, Mathieu Bahin, Sophie Foulon, Pablo Ibanez, Lluis Quintana-Murci, Tatsuhiko Ozawa, Sylvie van der Werf, Philippe Nghe, Nadia Naffakh, Andrew Griffiths, Catherine Isel
Publikováno v:
Proceedings of the National Academy of Sciences of the United States of America
Proceedings of the National Academy of Sciences of the United States of America, 2023, 120 (6), pp.e2211098120. ⟨10.1073/pnas.2211098120⟩
Proceedings of the National Academy of Sciences of the United States of America, 2023, 120 (6), pp.e2211098120. ⟨10.1073/pnas.2211098120⟩
International audience; The segmented RNA genome of influenza A viruses (IAVs) enables viral evolution through genetic reassortment after multiple IAVs coinfect the same cell, leading to viruses harboring combinations of eight genomic segments from d
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e1a6151b328050a32ee6cb40589637fd
https://doi.org/10.1073/pnas.2211098120
https://doi.org/10.1073/pnas.2211098120
Autor:
Vaitea Opuu, Giuliano Nigro, Christine Lazennec-Schurdevin, Yves Mechulam, Emmanuelle Schmitt, Thomas Simonson
Amino acids (AAs) with a noncanonical backbone would be a valuable tool for protein engineering, enabling new structural motifs and building blocks. To incorporate them into an expanded genetic code, the first, key step is to obtain an appropriate am
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::fb8721f59199db0e0a1725d6c0639059
https://doi.org/10.1101/2022.12.28.522074
https://doi.org/10.1101/2022.12.28.522074
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 2405
The design of proteins and miniproteins is an important challenge. Designed variants should be stable, meaning the folded/unfolded free energy difference should be large enough. Thus, the unfolded state plays a central role. An extended peptide model
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::efc71023018a6e970a3a6848f3576a6e
https://pubmed.ncbi.nlm.nih.gov/35298824
https://pubmed.ncbi.nlm.nih.gov/35298824
Autor:
Young Joo Sun, Carlos Corbi-Verge, Nicolas Panel, Vaitea Opuu, Philip M. Kim, Titus Hou, Thomas Simonson, Marcus B. Noyes, David M. Ichikawa, Ernesto J. Fuentes
Publikováno v:
Scientific Reports, Vol 10, Iss 1, Pp 1-9 (2020)
Scientific Reports
Scientific Reports, Nature Publishing Group, 2020, 10 (1), pp.11150. ⟨10.1038/s41598-020-67972-w⟩
Scientific Reports
Scientific Reports, Nature Publishing Group, 2020, 10 (1), pp.11150. ⟨10.1038/s41598-020-67972-w⟩
A powerful approach to understand protein structure and evolution is to perform computer simulations that mimic aspects of evolution. In particular, structure-based computational protein design (CPD) can address the inverse folding problem, exploring
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c547ce2f6433948eaa712562e8d22676
http://link.springer.com/article/10.1038/s41598-020-67972-w
http://link.springer.com/article/10.1038/s41598-020-67972-w
Publikováno v:
Methods in Molecular Biology ISBN: 9781071618547
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e121173e45fc3c811769ed9b124690c4
https://doi.org/10.1007/978-1-0716-1855-4_19
https://doi.org/10.1007/978-1-0716-1855-4_19
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 2256
This chapter describes two computational methods for PDZ-peptide binding: high-throughput computational protein design (CPD) and a medium-throughput approach combining molecular dynamics for conformational sampling with a Poisson-Boltzmann (PB) Linea
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::183f2ecf865e760e6042ae53bf3841ab
https://pubmed.ncbi.nlm.nih.gov/34014526
https://pubmed.ncbi.nlm.nih.gov/34014526
Publikováno v:
Methods in Molecular Biology ISBN: 9781071611654
This chapter describes two computational methods for PDZ-peptide binding: high-throughput computational protein design (CPD) and a medium-throughput approach combining molecular dynamics for conformational sampling with a Poisson-Boltzmann (PB) Linea
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f33316b1dd2e98061fe4fb5c915c653c
https://doi.org/10.1007/978-1-0716-1166-1_14
https://doi.org/10.1007/978-1-0716-1166-1_14