Concept

Structural bioinformatics

Related publications (32)

Predicting protein interactions using geometric deep learning on protein surfaces

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 the ...

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

Aptamer-Functionalized Interface Nanopores Enable Amino Acid-Specific Peptide Detection

Nako Nakatsuka, Xinyu Zhang, Haiying Hu

Single-molecule proteomics based on nanopore technology has made significant advances in recent years. However, to achieve nanopore sensing with single amino acid resolution, several bottlenecks must be tackled: controlling nanopore sizes with nanoscale pr ...

2024

Robust mass lumping and outlier removal strategies in isogeometric analysis

Annalisa Buffa, Espen Sande, Yannis Dirk Voet

Mass lumping techniques are commonly employed in explicit time integration schemes for problems in structural dynamics and both avoid solving costly linear systems with the consistent mass matrix and increase the critical time step. In isogeometric analysi ...

2024

A generic diffusion-based approach for 3D human pose prediction in the wild

Alexandre Massoud Alahi, Saeed Saadatnejad, Taylor Ferdinand Mordan

Predicting 3D human poses in real-world scenarios, also known as human pose forecasting, is inevitably subject to noisy inputs arising from inaccurate 3D pose estimations and occlusions. To address these challenges, we propose a diffusion-based approach th ...

IEEE2023

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

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

Structural topology exploration through policy-based generation of equilibrium representations

Corentin Jean Dominique Fivet, Ioannis Mirtsopoulos

Mainstream approaches to design spatial architectural forms that are structurally relevant consist either in adapting well-known and catalogued conventional types or in searching for close-to-optimum solutions of well-defined problems. Few means exist to e ...

2023

De novo design of protein interactions with learned surface fingerprints

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

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

Computational Conceptual Design – Typological Exploration Of Spatial Truss Systems Through Optimization

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

Exploring a wide range of relevant design options from the outset is crucial for every sound conceptual design process. Optimization techniques are generally employed to generate well-performing structural design options. However, focusing only on performa ...

2023

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