Publications related to Rosetta FunFolDes - A general framework for the computational design of functional proteins

Related publications (33)

NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual

Analyzing molecular surfaces to predict functional sites and identify protein cavities for small molecule binding is essential in structural biology and drug discovery, particularly when targeting allosteric sites or designing PROTACs. Moreover, measuring ...

American Chemical Society (ACS)2025

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

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

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

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

EPFL2024

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

The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation

Nagammal Neelagandan

Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the 16p11.2 microdeletion, bear no obvious connection to translation. Here, we use proteomics, g ...

Amer Assoc Advancement Science2024

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

EPFL2024

Antibodies expand the scope of angiotensin receptor pharmacology

Shuhao Zhang, Patrick Daniel Barth

G-protein-coupled receptors (GPCRs) are key regulators of human physiology and are the targets of many small-molecule research compounds and therapeutic drugs. While most of these ligands bind to their target GPCR with high affinity, selectivity is often l ...

2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Mohan Vamsi Nallapareddy, Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

Modified capillary number to standardize droplet generation in suction-driven microfluidics

Jatin Panwar

In droplet microfluidic devices with suction-based flow control, the microchannel geometry and suction pressure at the outlet govern the dynamic properties of the two phases that influence the droplet generation. Therefore, it is critical to understand the ...

Springer Heidelberg2024

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

Mechanisms and functions of protein S-acylation

Françoise Gisou van der Goot Grunberg, Laurence Gouzi Abrami, Francisco De Magalhães Sarmento Ribeiro De Mesquita

Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

Nature Portfolio2024

Prolamins' 3D structure: A new insight into protein modeling using the language of numbers and shapes

Niloufar Sharif

This study combined protein modeling methods to generate the prolamins' fractions as precise as possible. Hence, gliadins, zeins, kafirins, hordeins, secalins, avenins and oryzins were generated based on their characteristics and disulfide mapping. Finding ...

Elsevier Sci Ltd2024

RE:SLAB — a load bearing system for open-ended component reuse in building structures

Corentin Jean Dominique Fivet, Jan Friedrich Georg Brütting, Dario Redaelli, Alex-Manuel Muresan, Edisson Xavier Estrella Arcos

The construction industry plays a major role in the high levels of greenhouse gas emissions, resource consumption, and waste generation observed nowadays. Key to the circular economy, structural component reuse arises as a promising solution to divert cons ...

2024

Two-particle Bose-Einstein correlations and their Lévy parameters in PbPb collisions at √sNN=5.02 TeV

Jian Wang, Matthias Finger, Qian Wang, Yiming Li, João Miguel das Neves Duarte, Matthias Wolf, Varun Sharma, Yi Zhang, Tian Cheng, Yixing Chen, Alexis Kalogeropoulos, Ioannis Papadopoulos, Hua Zhang, Siyuan Wang, Xin Chen, Michele Bianco, Sebastiana Gianì, Sun Hee Kim, Davide Di Croce, Jian Zhao, Rakesh Chawla, Jan Steggemann, Konstantin Androsov, Anna Mascellani, Federica Legger, Matteo Galli, Gabriele Grosso

Two -particle Bose-Einstein momentum correlation functions are studied for charged-hadron pairs in lead -lead collisions at a center -of -mass energy per nucleon pair of .'/sNN = 5.02 TeV. The data sample, containing 4.27 x 109 minimum bias events correspo ...

Amer Physical Soc2024

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

Yanheng Guo

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

EPFL2024

Strategy to systematically design and deploy the ITER plasma control system: A system engineering and model-based design approach

Richard Pitts, Federico Alberto Alfredo Felici, Federico Pesamosca, Anna Ngoc Minh Trang Vu

The paper details the process of developing the ITER Plasma Control System (PCS), that is, how to design and deploy it systematically, in the most efficient and effective manner. The integrated nature of the ITER PCS, with its multitude of coupled control ...

Elsevier Science Sa2024

Recording physiological history of cells with chemical labeling

Kai Johnsson, Julien Hiblot

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins t ...

American Association for the Advancement of Science2024

A semantic model-based systems engineering approach for assessing the operational performance of metal forming process

Dimitrios Kyritsis, Jinzhi Lu

Metal Forming is a basic and essential industrial process to provide materials for constructing complex products. To design an efficient metal forming process, the functional requirements and operational performance are two important aspects to be consider ...

Pergamon-Elsevier Science Ltd2024