Publications associées à Amarrage macromoléculaire

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 th ...

EPFL2024

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

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Anne-Florence Raphaëlle Bitbol

Author summaryWhen two protein families interact, their sequences feature statistical dependencies. First, interacting proteins tend to share a common evolutionary history. Second, maintaining structure and interactions through the course of evolution yiel ...

PUBLIC LIBRARY SCIENCE2023

Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

Bruno Emanuel Ferreira De Sousa Correia, Anthony Marchand, Emmanuel Doram Levy, Xiao Wang

Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest ...

2023

Structural and functional characterisation of the KRAB-domain associated protein 1

Giulia Fonti

KAP1 (KRAB-domain associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular i ...

EPFL2019

KAP1 is an antiparallel dimer with a functional asymmetry

Didier Trono, Matteo Dal Peraro, Beat Fierz, Davide Demurtas, Louise Catherine Bryan, Maria Josefina Marcaida Lopez, Giulia Fonti, Pierre-Yves Joseph Laurent Helleboid, Alexandra Styliani Kalantzi

KAP1 (KRAB domain-associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular i ...

Life Science Alliance, LLC2019

Constrained optimization applied to multiscale integrative modeling

Giorgio Elikem Tamo

Multiscale integrative modeling stands at the intersection between experimental and computational techniques to predict the atomistic structures of important macromolecules. In the integrative modeling process, the experimental information is often integra ...

EPFL2018

DNA-BSA interaction, cytotoxicity and molecular docking of mononuclear zinc complexes with reductively cleaved N2S2 Schiff base ligands

Kurt Schenk, Farzaneh Fadaei Tirani

The synthesis of three potentially tetradentate, N2S2 Schiff-base-ligands, containing a disulfide bond, (LSSLThio)-S-Thio(L1), (LSSLBr)-S-Br(L2) and (LSSLDiMeO)-S-DiMeO (L3) are reported. These ligands undergo reductive disulfide bond scission upon reactio ...

ELSEVIER SCIENCE SA2018

Structural and functional analysis of host attachment proteins from contractile injection systems

Michel Plattner

Bacteriophages of the myoviridae family, R-type pyocin, Photorhabus virulence cassette (PVC), Serratia antifeeding prophage (Afp) and type 6 secretion system (T6SS) form a class of contractile injection systems that share common structural and functional c ...

EPFL2018

Computational design of environmental sensors for the potent opioid fentanyl

Kai Johnsson, Luc Reymond

We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to opt ...

Elife Sciences Publications Ltd2017