Concept

Lattice protein

Related publications (26)

Deep learning approaches for conformational flexibility and switching properties in protein design

Following the hugely successful application of deep learning methods to protein structure prediction, an increasing number of design methods seek to leverage generative models to design proteins with improved functionality over native proteins or novel str ...

2022

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

Jaume Bonet Martinez

Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...

OXFORD UNIV PRESS2021

Structure-Property Relationships in Complex Materials by Combining Supervised and Unsupervised Machine Learning

Benjamin Aaron Helfrecht

The work presented in this thesis combines supervised and unsupervised machine learning to examine structure-property relationships in databases of materials. While either supervised learning or unsupervised learning alone can be a powerful tool for assess ...

EPFL2021

Exploring the Molecular Conformation Space by Soft Molecule- Surface Collision

Klaus Kern, Stephan Rauschenbach, Sabine Abb

Biomolecules function by adopting multiple conformations. Such dynamics are governed by the conformation landscape whose study requires characterization of the ground and excited conformation states. Here, the conformational landscape of a molecule is samp ...

AMER CHEMICAL SOC2020

Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?

Matteo Dal Peraro, Luciano Andres Abriata

Protein dynamics is undoubtedly a pervasive ingredient in all biological functions. However, structural biology has been strongly driven by a static-centered view of protein architecture. We argue that the recent advances of cryo-electron microscopy (EM) h ...

AMER CHEMICAL SOC2020

Tuning Interaction Parameters of Thermoplastic Polyurethanes in a Binary Solvent To Achieve Precise Control over Microphase Separation

Oguzhan Oguz

Thermoplastic polyurethanes (TPUs) are designed using a large variety of basic building blocks but are only synthesized in a limited number of solvent systems. Understanding the behavior of the copolymers in a selected solvent system is of particular inter ...

AMER CHEMICAL SOC2019

Mid-Infrared plasmonic nanoantennas for ultrasensitive detection of proteins and their secondary structure

Dordaneh Etezadi

Engineered plasmonic nanostructures have emerged as powerful sensing platforms and are promoting novel applications in various fields. By providing extreme field confinement down to molecular dimensions and enhancing light-matter interaction at the nanosca ...

EPFL2018

Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution

Michele Ceriotti, Kevin Rossi

The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecul ...

American Institute of Physics2017

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Bruno Emanuel Ferreira De Sousa Correia, Stefano Zamuner

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based ...

Wiley-Blackwell2016

Mechanism to Trigger Unfolding in O6--Alkylguanine-DNA Alkyltransferase

Ursula Röthlisberger, Elizabeth Claire Brunk, Birgit Mollwitz

O6-alkylguanine-DNA alkyltransferase (AGT) adopts a non-enzymatic suicide mechanism for the repair of methylated guanine bases by transferring the methyl adduct to itself, thereby initiating unfolding and fast degradation. Classical molecular dynamics simu ...

Wiley-Blackwell2013

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