Publications by authors named "Alexander M Monzon"

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IDPEnsembleTools: An open-source library for analysis of conformational ensembles of disordered proteins.
Hamidreza Ghafouri, Giacomo Janson, Silvio C E Tosatto, Alexander Miguel Monzon

Protein Sci· January 2026

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Advances in the determination of disordered protein ensemble.
Hamidreza Ghafouri, Silvio C E Tosatto, Alexander Miguel Monzon

Curr Opin Struct Biol· December 2025

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AlphaFlex: Ensembles of the human proteome representing disordered regions.
Zi Hao Liu, Oufan Zhang, Stefano De Castro, Kunyang Sun, Hamidreza Ghafouri, Alexander M Monzon

bioRxiv· November 2025

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GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins.
Zarifa Osmanli, Elisa Ferrero, Alexander Miguel Monzon, Silvio C E Tosatto, Damiano Piovesan

Bioinformatics· July 2025

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ngx-mol-viewers: Angular components for interactive molecular visualization in bioinformatics.
Damiano Clementel, Alessio Del Conte, Alexander Miguel Monzon, Silvio C E Tosatto

Front Bioinform· June 2025

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DRMAAtic: dramatically improve your cluster potential.
Alessio Del Conte, Hamidreza Ghafouri, Damiano Clementel, Ivan Mičetić, Damiano Piovesan, Alexander Miguel Monzon

Bioinform Adv· May 2025

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RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB.
Damiano Clementel, Paula Nazarena Arrías, Soroush Mozaffari, Zarifa Osmanli, Ximena Aixa Castro, Alexander Miguel Monzon

Nucleic Acids Res· January 2025

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Searching and Using MobiDB Resource 6 to Explore Predictions and Annotations for Intrinsically Disordered Proteins.
Maria Cristina Aspromonte, Federica Quaglia, Alexander Miguel Monzon, Damiano Clementel, Alessio Del Conte

Curr Protoc· December 2024

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Diversity and structural-functional insights of alpha-solenoid proteins.
Paula Nazarena Arrías, Zarifa Osmanli, Estefanía Peralta, Patricio Manuel Chinestrad, Alexander Miguel Monzon

Protein Sci· November 2024

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STRPsearch: fast detection of structured tandem repeat proteins.
Soroush Mozaffari, Paula Nazarena Arrías, Damiano Clementel, Damiano Piovesan, Carlo Ferrari, Alexander Miguel Monzon

Bioinformatics· November 2024

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RING 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures.
Alessio Del Conte, Giorgia F Camagni, Damiano Clementel, Giovanni Minervini, Alexander Miguel Monzon

Nucleic Acids Res· July 2024

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Structured Tandem Repeats in Protein Interactions.
Juan Mac Donagh, Abril Marchesini, Agostina Spiga, Maximiliano José Fallico, Paula Nazarena Arrías, Alexander Miguel Monzon

Int J Mol Sci· March 2024

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CAFA-evaluator: a Python tool for benchmarking ontological classification methods.
Damiano Piovesan, Davide Zago, Parnal Joshi, M Clara De Paolis Kaluza, Mahta Mehdiabadi, Alexander Miguel Monzon

Bioinform Adv· March 2024

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PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins.
Hamidreza Ghafouri, Tamas Lazar, Alessio Del Conte, Luiggi G Tenorio Ku, , Alexander Miguel Monzon

Nucleic Acids Res· January 2024

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DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology.
Omar Abdelghani Attafi, Damiano Clementel, Konstantinos Kyritsis, Emidio Capriotti, Gavin Farrell, Alexander Miguel Monzon

Gigascience· January 2024

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A STRP-ed definition of Structured Tandem Repeats in Proteins.
Alexander Miguel Monzon, Paula Nazarena Arrías, Arne Elofsson, Pablo Mier, Miguel A Andrade-Navarro

J Struct Biol· December 2023

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The repetitive structure of DNA clamps: An overlooked protein tandem repeat.
Paula Nazarena Arrías, Alexander Miguel Monzon, Damiano Clementel, Soroush Mozaffari, Damiano Piovesan

J Struct Biol· September 2023

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CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins.
Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon

Nucleic Acids Res· July 2023

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RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics.
Alessio Del Conte, Alexander Miguel Monzon, Damiano Clementel, Giorgia F Camagni, Giovanni Minervini

Bioinformatics· May 2023

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Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS-Q.
Nahuel Escobedo, Alexander Miguel Monzon, María Silvina Fornasari, Nicolas Palopoli, Gustavo Parisi

Curr Protoc· May 2023

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MobiDB: 10 years of intrinsically disordered proteins.
Damiano Piovesan, Alessio Del Conte, Damiano Clementel, Alexander Miguel Monzon, Martina Bevilacqua

Nucleic Acids Res· January 2023

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Intrinsic protein disorder and conditional folding in AlphaFoldDB.
Damiano Piovesan, Alexander Miguel Monzon, Silvio C E Tosatto

Protein Sci· November 2022

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CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure.
Nahuel Escobedo, Ronaldo Romario Tunque Cahui, Gastón Caruso, Emilio García Ríos, Layla Hirsh, Alexander Miguel Monzon

Bioinformatics· October 2022

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RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles.
Damiano Clementel, Alessio Del Conte, Alexander Miguel Monzon, Giorgia F Camagni, Giovanni Minervini

Nucleic Acids Res· July 2022

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Databases for intrinsically disordered proteins.
Damiano Piovesan, Alexander Miguel Monzon, Federica Quaglia, Silvio C E Tosatto

Acta Crystallogr D Struct Biol· February 2022

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