AT
Antonio Trovato
cond-mat.stat-mechcond-mat.softq-bio.BMModels, ChemicalModels, MolecularProtein FoldingbiophysicsQuorum SensingAlgorithmsAmyloid
On Valency
published · living versionsW_bz4z2z6r·v1 · currentpublished
An Empirical Study on Clustering-based Quantum Approximate Optimization Algorithm for Regression Test Case Selection
with Martin Beseda, Dario Di Nucci
1 version
Preprints & journals
59 papers in the corpus · 1998–2026Meso-Soup: A community approach to building a computational description of the biological mesoscale.42515870 · Harris, Sarah Anne, Lattanzi, Gianluca, Rosa, Angelo et al.2026 · 0 citationsBiophysical journal. 2026;125(17):4528-4540
Quantum algorithms for compact polymer thermodynamics2603.12334v1 · Davide Rattacaso, Daniel Jaschke, Antonio Trovato et al.2026 · 0 citationsarXiv
Structural commonalities determined by physicochemical principles in the complex polymorphism of the amyloid state of proteins.39693572 · Errico, Silvia, Fani, Giulia, Ventura, Salvador et al.2025 · 14 citationsThe Biochemical journal. 2025;482(2):87-101
A scale-invariant log-normal droplet size distribution below the critical concentration for protein phase separation.39556435 · Amico, Tommaso, Dada, Samuel Toluwanimi, Lazzari, Andrea et al.2024 · 3 citationseLife. 2024;13
Folding kinetics of an entangled protein.37956216 · Salicari, Leonardo, Baiesi, Marco, Orlandini, Enzo et al.2023 · 10 citationsPLoS computational biology. 2023;19(11):e1011107
Entangled Motifs in Membrane Protein Structures.37298146 · Salicari, Leonardo, Trovato, Antonio2023 · 5 citationsInternational journal of molecular sciences. 2023;24(11)
A scale-invariant log-normal droplet size distribution below the critical concentration for protein phase separation10.1101/2023.04.11.536478v3 · Amico, T., Dada, S., Lazzari, A. et al.2023 · 10 citationsbioRxiv
Key interaction patterns in proteins revealed by cluster expansion of the partition function.36447074 · Tajana, Matteo, Trovato, Antonio, Tiana, Guido2022 · 0 citationsThe European physical journal. E, Soft matter. 2022;45(11):95
Sequence-Based Prediction of Protein Phase Separation: The Role of Beta-Pairing Propensity.36551199 · Mullick, Pratik, Trovato, Antonio2022 · 8 citationsBiomolecules. 2022;12(12)
Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules.35085247 · Zamuner, Stefano, Seno, Flavio, Trovato, Antonio2022 · 1 citationPloS one. 2022;17(1):e0254969
Sequence based prediction of protein phase separation into disordered condensates using machine learning10.1101/2021.12.13.472521v1 · Mullick, P., Trovato, A.2021 · 3 citationsbioRxiv
Sequence and structural patterns detected in entangled proteins reveal the importance of co-translational folding.31182755 · Baiesi, Marco, Orlandini, Enzo, Seno, Flavio et al.2020 · 57 citationsScientific reports. 2019;9(1):8426
Signature of Pareto optimization in the Escherichia coli proteome.29904084 · Koçillari, Loren, Fariselli, Piero, Trovato, Antonio et al.2019 · 175 citationsScientific reports. 2018;8(1):9141
Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes.29318668 · Škrbić, Tatjana, Zamuner, Stefano, Hong, Rolando et al.2019 · 5 citationsProteins. 2018;86(4):393-404
Bacterial bioluminescence onset and quenching: a dynamical model for a quorum sensing-mediated property.29308273 · Side, Domenico Delle, Nassisi, Vincenzo, Pennetta, Cecilia et al.2020 · 11 citationsRoyal Society open science. 2017;4(12):171586
Exploring the correlation between the folding rates of proteins and the entanglement of their native states1709.01815v2 · Marco Baiesi, Enzo Orlandini, Flavio Seno et al.2017 · 57 citationsJ. Phys. A: Math. Theor. 50 (2017) 504001 (16pp)
Bubble-bound state of triple-stranded DNA: Efimov Physics in DNA with repulsion1703.09432v1 · Jaya Maji, Flavio Seno, Antonio Trovato et al.2017 · 6 citationsarXiv
Modeling quorum sensing trade-offs between bacterial cell density and system extension from open boundaries.27966657 · Marenda, Mattia, Zanardo, Marina, Trovato, Antonio et al.2018 · 22 citationsScientific reports. 2016;6:39142
Linking in domain-swapped protein dimers.27659606 · Baiesi, Marco, Orlandini, Enzo, Trovato, Antonio et al.2023 · 45 citationsScientific reports. 2016;6:33872
An efficient algorithm to perform local concerted movements of a chain molecule.25825903 · Zamuner, Stefano, Rodriguez, Alex, Seno, Flavio et al.2016 · 46 citationsPloS one. 2015;10(3):e0118342
Native fold and docking pose discrimination by the same residue-based scoring function.25619680 · Sarti, Edoardo, Granata, Daniele, Seno, Flavio et al.2015 · 17 citationsProteins. 2015;83(4):621-30
PASTA 2.0: an improved server for protein aggregation prediction.24848016 · Walsh, Ian, Seno, Flavio, Tosatto, Silvio C E et al.2014 · 473 citationsNucleic acids research. 2014;42(Web Server issue):W301-7
Quorum vs. diffusion sensing: a quantitative analysis of the relevance of absorbing or reflecting boundaries.24484313 · Trovato, Antonio, Seno, Flavio, Zanardo, Marina et al.2014 · 47 citationsFEMS microbiology letters. 2014;352(2):198-203
Melting behavior and different bound states in three-stranded DNA models.24580186 · Maji, Jaya, Bhattacharjee, Somendra M, Seno, Flavio et al.2015 · 9 citationsPhysical review. E, Statistical, nonlinear, and soft matter physics. 2014;89(1):012121
Sequence repeats and protein structure.23214731 · Hoang, Trinh X, Trovato, Antonio, Seno, Flavio et al.2013 · 2 citationsPhysical review. E, Statistical, nonlinear, and soft matter physics. 2012;86(5 Pt 1):050901
Protein sequence and structure: Is one more fundamental than the other?1204.2725v1 · Jayanth R. Banavar, Trinh X. Hoang, Flavio Seno et al.2012 · 5 citationsarXiv
Fibril elongation mechanisms of HET-s prion-forming domain: topological evidence for growth polarity.21989930 · Baiesi, Marco, Seno, Flavio, Trovato, Antonio2012 · 8 citationsProteins. 2011;79(11):3067-81
Exploring the universe of protein structures beyond the Protein Data Bank.21079678 · Cossio, Pilar, Trovato, Antonio, Pietrucci, Fabio et al.2011 · 73 citationsPLoS computational biology. 2010;6(11):e1000957
Simplified exactly solvable model for β-amyloid aggregation.20867550 · Zamparo, M, Trovato, A, Maritan, A2011 · 15 citationsPhysical review letters. 2010;105(10):108102
When a DNA Triple helix melts: An analog of the Efimov state1005.3628v3 · Jaya Maji, Somendra M. Bhattacharjee, Flavio Seno et al.2010 · 20 citationsNew J. Phys.12:083057, 2010
Different pulling modes in DNA overstretching: a theoretical analysis.20866280 · Marenduzzo, D, Orlandini, E, Seno, F et al.2011 · 16 citationsPhysical review. E, Statistical, nonlinear, and soft matter physics. 2010;81(5 Pt 1):051926
A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation.19680431 · Auer, Stefan, Trovato, Antonio, Vendruscolo, Michele2009 · 102 citationsPLoS computational biology. 2009;5(8):e1000458
Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses.19602727 · Cendron, Laura, Trovato, Antonio, Seno, Flavio et al.2009 · 49 citationsThe Journal of biological chemistry. 2009;284(38):25832-41
REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform.19478001 · Marsella, Luca, Sirocco, Francesco, Trovato, Antonio et al.2009 · 62 citationsBioinformatics (Oxford, England). 2009;25(12):i289-95
Consequences of relative cellular positioning on quorum sensing and bacterial cell-to-cell communication.19187204 · Alberghini, Sara, Polone, Elisa, Corich, Viviana et al.2009 · 67 citationsFEMS microbiology letters. 2009;292(2):149-61
Melting a stretched DNA0807.3236v1 · D. Marenduzzo, A. Maritan, E. Orlandini et al.2008 · 1 citationarXiv
Inference of the solvation energy parameters of amino acids using maximum entropy approach.18647046 · Hoang, Trinh X, Seno, Flavio, Trovato, Antonio et al.2008 · 4 citationsThe Journal of chemical physics. 2008;129(3):035102
Emergence of secondary motifs in tubelike polymers in a solvent.18643292 · Poletto, Chiara, Giacometti, Achille, Trovato, Antonio et al.2008 · 15 citationsPhysical review. E, Statistical, nonlinear, and soft matter physics. 2008;77(6 Pt 1):061804
Maximum entropy approach for deducing amino Acid interactions in proteins.18352600 · Seno, Flavio, Trovato, Antonio, Banavar, Jayanth R et al.2008 · 44 citationsPhysical review letters. 2008;100(7):078102
Symmetry, shape, and order.18032605 · Trovato, Antonio, Hoang, Trinh Xuan, Banavar, Jayanth R et al.2008 · 17 citationsProceedings of the National Academy of Sciences of the United States of America. 2007;104(49):19187-92
Structural motifs of biomolecules.17959779 · Banavar, Jayanth R, Hoang, Trinh Xuan, Maddocks, John H et al.2007 · 33 citationsProceedings of the National Academy of Sciences of the United States of America. 2007;104(44):17283-6
The PASTA server for protein aggregation prediction.17720750 · Trovato, Antonio, Seno, Flavio, Tosatto, Silvio C E2008 · 244 citationsProtein engineering, design & selection : PEDS. 2007;20(10):521-3
Simple solvation potential for coarse-grained models of proteins.17286285 · Bhattacharyay, A, Trovato, A, Seno, F2007 · 4 citationsProteins. 2007;67(2):285-92
Insight into the structure of amyloid fibrils from the analysis of globular proteins.17173479 · Trovato, Antonio, Chiti, Fabrizio, Maritan, Amos et al.2007 · 203 citationsPLoS computational biology. 2006;2(12):e170
Common attributes of native-state structures of proteins, disordered proteins, and amyloid.16624879 · Hoang, Trinh X, Marsella, Luca, Trovato, Antonio et al.2006 · 47 citationsProceedings of the National Academy of Sciences of the United States of America. 2006;103(18):6883-8
Geometry of proteins: hydrogen bonding, sterics, and marginally compact tubes.16605572 · Banavar, Jayanth R, Cieplak, Marek, Flammini, Alessandro et al.2006 · 14 citationsPhysical review. E, Statistical, nonlinear, and soft matter physics. 2006;73(3 Pt 1):031921
Physics of thick polymerscond-mat/0508446v1 · D. Marenduzzo, A. Flammini, A. Trovato et al.2005 · 23 citationsJ. Pol. Sci. B 43, 650-679 (2005)
Design of amino acid sequences to fold into C(alpha)-model proteins.16108690 · Amatori, A, Tiana, G, Sutto, L et al.2007 · 4 citationsThe Journal of chemical physics. 2005;123(5):054904
Continuum model for polymers with finite thicknesscond-mat/0503596v1 · D. Marenduzzo, C. Micheletti, H.Seyed-allaei et al.2005 · 19 citationsarXiv
Geometrical model for the native-state folds of proteins.15752620 · Trinh, X Hoang, Trovato, Antonio, Seno, Flavio et al.2005 · 9 citationsBiophysical chemistry. 2005;115(2-3):289-94
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