Publications related to Lattice protein

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

Patrick Daniel Barth, Lucas Sebastian Powell-Rudden, Mahdi Hijazi

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

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

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

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

Highly Specific Methods for the Prediction of Genes Regulated by MicroRNAs

Ray Marcel Marin Florez

MicroRNAs (miRNAs) comprise a large set of short noncoding RNAs that bind to messenger RNAs (mRNAs) to reduce their translation into functional proteins. Computational prediction of miRNA targets is the first stage in the discovery and validation of new re ...

EPFL2012

Structural Preferences of Gas-Phase M2TMP Monomers upon Sequence Variations

Yury Tsybin, Hisham Ben Hamidane, Rodolphe Antoine

The conformations of a number of M2TMP-(22-46) sequence variants have been investigated using ion mobility spectrometry (IMS). Substantial conformational changes were evidenced by IMS upon the variation of a single amino acid in the peptide sequence, with ...

2011

Tunable and Broadband Nanostructured Photonic Devices : Fabrication and Characterization

Pierre-Yves Baroni

The main topic of this thesis is the fabrication and characterization of structures smaller than the wavelength of light, for operation in the visible or near infrared spectral range. In the first part of this thesis, the fabrication of periodic structures ...

EPFL2010

Solute energy based REMD : developments and applications to prion protein misfold predictions

Molecular dynamics (MD) simulations have increasingly contributed to the understanding of biomolecular processes, allowing for predictions of thermodynamic and structural properties. Unfortunately, the holy grail of protein structure prediction was soon fo ...

EPFL2008

Switch peptides : a new tool for the study of ß sheet aggregation and the design of novel ß breakers

Incorrect folding of proteins, leading to aggregation and amyloid formation, is associated with a group of degenerative diseases including Alzheimer's disease and late onset diabetes. Amyloid forming proteins are believed to be mainly α-helical in their na ...

EPFL2006

On the structural stability of the free and metal-loaded c-terminal domain of the prion protein

Maria Carola Colombo

A misfolded conformer of the cellular prion protein, denoted as scrapie prion protein, is considered responsible for a variety of fatal neurodegenerative diseases. Both, the function of the protein in its native conformation as well as the factors that tri ...

EPFL2006