Publications by authors named "Simon Poblete"

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Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.
Rachael C Kretsch, Elisa Posani, Eugene F Baulin, Janusz M Bujnicki, Giovanni Bussi, Simón Poblete

Proteins· January 2026

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AbAgym: a well-curated dataset for the mutational analysis of antibody-antigen complexes.
Gabriel Cia, Dong Li, Simón Poblete, Marianne Rooman, Fabrizio Pucci

MAbs· December 2025

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Blind prediction of complex water and ion ensembles around RNA in CASP16.
Rachael C Kretsch, Elisa Posani, Eugene F Baulin, Janusz M Bujnicki, Giovanni Bussi, Simón Poblete

bioRxiv· November 2025

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Unknotting RNA: A method to resolve computational artifacts.
Simón Poblete, Mikolaj Mlynarczyk, Marta Szachniuk

PLoS Comput Biol· March 2025

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RNA-Puzzles Round V: blind predictions of 23 RNA structures.
Fan Bu, Yagoub Adam, Ryszard W Adamiak, Maciej Antczak, Belisa Rebeca H de Aquino, Simón Poblete

Nat Methods· February 2025

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Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.
Bernhard C Thiel, Giovanni Bussi, Simón Poblete, Ivo L Hofacker

Nucleic Acids Res· September 2024

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The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline.
Bernhard C Thiel, Simón Poblete, Ivo L Hofacker

Methods Mol Biol· May 2024

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Editorial: Recent advances in computational modelling of biomolecular complexes.
Simón Poblete, Sergio Pantano, Kei-Ichi Okazaki, Zhongjie Liang, Kurt Kremer

Front Chem· April 2023

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RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates.
Simón Poblete, Anže Božič, Matej Kanduč, Rudolf Podgornik, Horacio V Guzman

ACS Omega· December 2021

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Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models.
Simón Poblete, Horacio V Guzman

Viruses· August 2021

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Brief Comparison between Experimental and Computationally Generated Ensembles of RNA Dinucleotides.
Simón Poblete, Tomás Pérez-Acle

J Chem Inf Model· February 2020

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RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Jiří Šponer, Giovanni Bussi, Miroslav Krepl, Pavel Banáš, Sandro Bottaro, Simón Poblete

Chem Rev· April 2018

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Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics.
Simón Poblete, Sandro Bottaro, Giovanni Bussi

Biochem Biophys Res Commun· March 2018

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A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.
Simón Poblete, Sandro Bottaro, Giovanni Bussi

Nucleic Acids Res· February 2018

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Static and dynamic light scattering by red blood cells: A numerical study.
Johannes Mauer, Matti Peltomäki, Simón Poblete, Gerhard Gompper, Dmitry A Fedosov

PLoS One· September 2017

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Single-Molecule FRET Measurements in Additive-Enriched Aqueous Solutions.
Daryan Kempe, Michele Cerminara, Simón Poblete, Antonie Schöne, Matteo Gabba

Anal Chem· January 2017

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Inter-dye distance distributions studied by a combination of single-molecule FRET-filtered lifetime measurements and a weighted accessible volume (wAV) algorithm.
Henning Höfig, Matteo Gabba, Simón Poblete, Daryan Kempe, Jörg Fitter

Molecules· November 2014

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Conformational state distributions and catalytically relevant dynamics of a hinge-bending enzyme studied by single-molecule FRET and a coarse-grained simulation.
Matteo Gabba, Simón Poblete, Tobias Rosenkranz, Alexandros Katranidis, Daryan Kempe

Biophys J· October 2014

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Hydrodynamics of discrete-particle models of spherical colloids: a multiparticle collision dynamics simulation study.
Simón Poblete, Adam Wysocki, Gerhard Gompper, Roland G Winkler

Phys Rev E Stat Nonlin Soft Matter Phys· September 2014

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Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase.
Liang Hong, Melissa A Sharp, Simón Poblete, Ralf Biehl, Michaela Zamponi

Biophys J· July 2014

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Coupling different levels of resolution in molecular simulations.
Simón Poblete, Matej Praprotnik, Kurt Kremer, Luigi Delle Site

J Chem Phys· March 2010

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