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A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

Publications associées (32)

De novo designed proteins: a study in engineering novel folds and functions

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023

NMR Crystallography in the Big Data Era: New Methods and Applications Powered by Machine Learning

Manuel Cordova

Structure determination of materials is key to understanding their physical properties. While single-crystal X-ray diffraction is the gold standard for structures displaying long-range order, many materials of interest are polycrystalline and/or disordered ...

EPFL2023

Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy

Marta Di Fabrizio

All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the prot ...

MDPI2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

De novo design of protein interactions with learned surface fingerprints

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Charlène Mireille Raymonde Raclot, Sandrine Madeleine Suzanne Georgeon, Beat Fierz, Aaron Simone Petruzzella, Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Stéphane Rosset, Alexandra Krina Van Hall-Beauvais, Alexandra Teslenko, Jane Marsden, Michael Bronstein, Casper Alexander Goverde, Stephen Michael Buckley, Dongchun Ni, Martin Pacesa

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

2023

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers

Camila Bacellar Cases Da Silveira, Christoph Bostedt

Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we ...

Nature Portfolio2023

A structured prediction approach for robot imitation learning

Aude Billard, Iason Batzianoulis, Anqing Duan

We propose a structured prediction approach for robot imitation learning from demonstrations. Among various tools for robot imitation learning, supervised learning has been observed to have a prominent role. Structured prediction is a form of supervised le ...

Sage Publications Ltd2023

Chemical Shift-Dependent Interaction Maps in Molecular Solids

Manuel Cordova, David Lyndon Emsley

Structure determinationof molecular solids through NMR crystallographyrelies on the generation of a comprehensive set of candidate crystalstructures and on the comparison of chemical shifts computed for thosecandidates with experimental values. Exploring t ...

AMER CHEMICAL SOC2023

Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

Andreas Füglistaler, Aurélien Laurent Jean-Charles Oggier, Mahdi Hijazi, Patrick Daniel Barth, Robert Everett Jefferson, Ana Paola Rico Villarreal

Engineering protein biosensors that sensitively respond to specific biomolecules by triggering precise cellular responses is a major goal of diagnostics and synthetic cell biology. Previous biosensor designs have largely relied on binding structurally well ...

Nature Research2023

Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

Ghérici Hassaïne

Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approa ...

Nature Portfolio2023

Computational conceptual design — typological exploration of spatial truss systems through optimization

Corentin Jean Dominique Fivet, Jonas Warmuth, Pierluigi D'Acunto

Exploring a wide range of design options is crucial for every sound conceptual design process. In the conventional structural design workflow, optimization techniques are generally employed to generate well-performing design options. However, focusing only ...

International Association for Shell and Spatial Structures (IASS)2023