Publications by authors named "David Simoncini"

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Complete combinatorial mutational enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity.
Mireia Solà Colom, Jelena Vučinić, Jared Adolf-Bryfogle, James W Bowman, Sébastien Verel, David Simoncini

Protein Sci· August 2024

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Artificial intelligence-based prediction models for acute myeloid leukemia using real-life data: A DATAML registry study.
Ibrahim Didi, Jean-Marc Alliot, Pierre-Yves Dumas, François Vergez, Suzanne Tavitian, David Simoncini

Leuk Res· January 2024

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Complete Combinatorial Mutational Enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity.
Mireia Solà Colom, Jelena Vucinic, Jared Adolf-Bryfogle, James W Bowman, Sébastien Verel, David Simoncini

Res Sq· September 2023

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Iterated local search with partition crossover for computational protein design.
François Beuvin, Simon de Givry, Thomas Schiex, Sébastien Verel, David Simoncini

Proteins· November 2021

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Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.
Sota Yagi, Aditya K Padhi, Jelena Vucinic, Sophie Barbe, Thomas Schiex, David Simoncini

J Am Chem Soc· October 2021

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Positive multistate protein design.
Jelena Vucinic, David Simoncini, Manon Ruffini, Sophie Barbe, Thomas Schiex

Bioinformatics· January 2020

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A structural homology approach for computational protein design with flexible backbone.
David Simoncini, Kam Y J Zhang, Thomas Schiex, Sophie Barbe

Bioinformatics· July 2019

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Computational design of symmetrical eight-bladed β-propeller proteins.
Hiroki Noguchi, Christine Addy, David Simoncini, Staf Wouters, Bram Mylemans

IUCrJ· January 2019

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Evolution-Inspired Computational Design of Symmetric Proteins.
Arnout R D Voet, David Simoncini, Jeremy R H Tame, Kam Y J Zhang

Methods Mol Biol· January 2018

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Fragger: a protein fragment picker for structural queries.
Francois Berenger, David Simoncini, Arnout Voet, Rojan Shrestha, Kam Y J Zhang

F1000Res· September 2017

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Balancing exploration and exploitation in population-based sampling improves fragment-based de novo protein structure prediction.
David Simoncini, Thomas Schiex, Kam Y J Zhang

Proteins· May 2017

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Guaranteed Discrete Energy Optimization on Large Protein Design Problems.
David Simoncini, David Allouche, Simon de Givry, Céline Delmas, Sophie Barbe

J Chem Theory Comput· December 2015

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Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method.
David Simoncini, Hiroya Nakata, Koji Ogata, Shinichiro Nakamura, Kam Yj Zhang

Mol Inform· February 2015

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Computational design of a self-assembling symmetrical β-propeller protein.
Arnout R D Voet, Hiroki Noguchi, Christine Addy, David Simoncini, Daiki Terada

Proc Natl Acad Sci U S A· October 2014

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Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm.
David Simoncini, Kam Y J Zhang

PLoS One· March 2014

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A probabilistic fragment-based protein structure prediction algorithm.
David Simoncini, Francois Berenger, Rojan Shrestha, Kam Y J Zhang

PLoS One· December 2012

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Error-estimation-guided rebuilding of de novo models increases the success rate of ab initio phasing.
Rojan Shrestha, David Simoncini, Kam Y J Zhang

Acta Crystallogr D Biol Crystallogr· November 2012

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Durandal: fast exact clustering of protein decoys.
Francois Berenger, Rojan Shrestha, Yong Zhou, David Simoncini, Kam Y J Zhang

J Comput Chem· February 2012

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