Publications related to On the origin of the boson peak in globular proteins

Related publications (35)

Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases

The R257(8)C mutation in smooth muscle actins, ACTG2 and ACTA2, is the most frequent cause of severe genetic diseases: namely, visceral myopathy, and familial thoracic aortic aneurysms and dissections, which respectively, stem from impairment of the viscer ...

ELSEVIER2025

G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction

Matteo Dal Peraro

Protein–ligand interactions (PLIs) determine the efficacy and safety profiles of small molecule drugs. Existing methods rely on either structural information or resource-intensive computations to predict PLI, casting doubt on whether it is possible to perf ...

2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

A Versatile Method for Site-Specific Chemical Installation of Aromatic Posttranslational Modification Analogs into Proteins

Bouchra Bouri, Hilal Lashuel, Rajasekhar Kolla, Shaswati Mandal

Posttranslational modifications (PTMs) of proteins play central roles in regulating the protein structure, interactome, and functions. A notable modification site is the aromatic side chain of Tyr, which undergoes modifications such as phosphorylation and ...

2024

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

Koopman-based Data-driven Robust Control of Nonlinear Systems Using Integral Quadratic Constraints

Alireza Karimi, Mert Eyuboglu

This paper introduces a novel method for data-driven robust control of nonlinear systems based on the Koopman operator, utilizing Integral Quadratic Constraints (IQCs). The Koopman operator theory facilitates the linear representation of nonlinear system d ...

2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

Structural heterogeneity of the ion and lipid channel TMEM16F

Horst Arthur Vogel

Transmembrane protein 16 F (TMEM16F) is a Ca2+-activated homodimer which functions as an ion channel and a phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, the mechanism of activation ...

Nature Portfolio2024

Observation of muonic Dalitz decays of chib mesons and precise spectroscopy of hidden-beauty states

Olivier Schneider, Aurelio Bay, Guido Haefeli, Tatsuya Nakada, Frédéric Blanc, Lesya Shchutska, Elena Graverini, Sebastian Schulte, Donal Patrick Hill, Marie Theres Christin Bachmayer, Serhii Cholak, Ettore Zaffaroni, Aravindhan Venkateswaran, Luis Miguel Garcia Martin, Vitalii Lisovskyi, Elisabeth Maria Niel, Federico Ronchetti, Radoslav Marchevski, Anni Matilda Kauniskangas, Dimitrios Kaminaris, Raphaël van Laak, Pierre Paul Louis Mayencourt, Brianna Leililani Thielen, Arnaud Merlin Gauthey, Gianluca Zunica, Abdul-Kerim Guseinov, Esteban Curras Rivera, Roberto Ribatti, Alexandre Brea Rodriguez, Rita De Sousa Ataíde Da Silva

The decays of the χb1(1P), χb2(1P), χb1(2P) and χb2(2P) mesons into the Υ(1S)μ+μ− final state are observed with a high significance using proton-proton collision data collected with the LHCb detector and corresponding to an integrated luminosity of 9 fb−1. ...

Springer Nature2024

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

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

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

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

A new age in protein design empowered by deep learning

Bruno Emanuel Ferreira De Sousa Correia, Michael Bronstein, Casper Alexander Goverde, Arne Schneuing, Hamed Khakzad, Ilia Igashov

The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

Cell Press2023

Writing and Drawing Inventions: Patents and Technology in France and the United States (18th-19th centuries)

Jérôme Baudry

Description (through texts, images, models or samples) played a central role in the patent regimes that emerged in the eighteenth century, first in England, later in the United States and in France. Description ensured that the contract—protection in excha ...

2023

Improving Standard-Cell Design Flow using Factored Form Optimization

Giovanni De Micheli, Alessandro Tempia Calvino

Factored form is a powerful multi-level representation of a Boolean function that readily translates into an implementation of the function in CMOS technology. In particular, the number of literals in a factored form correlates strongly with the number of ...

IEEE2023

Learning V1 Simple Cells with Vector Representation of Local Content and Matrix Representation of Local Motion

Yufan Ren

This paper proposes a representational model for image pairs such as consecutive video frames that are related by local pixel displacements, in the hope that the model may shed light on motion perception in primary visual cortex (V1). The model couples the ...

ASSOC ADVANCEMENT ARTIFICIAL INTELLIGENCE2022

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Lucien Fabrice Krapp

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

Reduced order modelling of nonaffine problems on parameterized NURBS multipatch geometries

Annalisa Buffa, Pablo Antolin Sanchez, Margarita Chasapi

This contribution explores the combined capabilities of reduced basis methods and IsoGeometric Analysis (IGA) in the context of parameterized partial differential equations. The introduction of IGA enables a unified simulation framework based on a single g ...

2022

De novo protein design by inversion of the AlphaFold structure prediction network

Benedict Dieter Gregor Wolf, Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset, Casper Alexander Goverde, Hamed Khakzad

De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in comp ...

2023

Reduced representations of complexes, signals, and multifiltrations

Celia Camille Hacker

The field of computational topology has developed many powerful tools to describe the shape of data, offering an alternative point of view from classical statistics. This results in a variety of complex structures that are not always directly amenable for ...

EPFL2022