Protein folding using inter-residue contacts. - Michele Vendruscolo (3DPVT, 2002)

Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils. - Mookyung Cheon; Iksoo Chang; Sandipan Mohanty; Leila M. Luheshi; Christopher M. Dobson; Michele Vendruscolo; Giorgio Favrin (PLoS Comput. Biol., 2007)

Competition between protein aggregation and protein complex formation. - Sebastian Pechmann; Emmanuel D. Levy; Gian Gaetano Tartaglia; Michele Vendruscolo (BMC Bioinform., 2008)

A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates. - Stefan Auer; Filip Meersman; Christopher M. Dobson; Michele Vendruscolo (PLoS Comput. Biol., 2008)

Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms. - Tammy M. K. Cheng; Yu-En Lu; Michele Vendruscolo; Pietro Liò; Tom L. Blundell (PLoS Comput. Biol., 2008)

A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation. - Stefan Auer; Antonio Trovato; Michele Vendruscolo (PLoS Comput. Biol., 2009)

Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation. - Anthony W. Fitzpatrick; Tuomas P. J. Knowles; Christopher A. Waudby; Michele Vendruscolo; Christopher M. Dobson (PLoS Comput. Biol., 2011)

ALMOST: An all atom molecular simulation toolkit for protein structure determination. - Biao Fu; Aleksandr B. Sahakyan; Carlo Camilloni; Gian Gaetano Tartaglia; Emanuele Paci; Amedeo Caflisch; Michele Vendruscolo; Andrea Cavalli (J. Comput. Chem., 2014)

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. - Mihaly Varadi; Simone Kosol; Pierre Lebrun; Erica Valentini; Martin Blackledge; A. Keith Dunker; Isabella C. Felli; Julie D. Forman-Kay; Richard W. Kriwacki; Roberta Pierattelli; Joel L. Sussman; Dmitri I. Svergun; et al. (Nucleic Acids Res., 2014)

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations. - Predrag Kukic; Arvind Kannan; Maurits J. J. Dijkstra; Sanne Abeln; Carlo Camilloni; Michele Vendruscolo (PLoS Comput. Biol., 2015)

Parapred: antibody paratope prediction using convolutional and recurrent neural networks. - Edgar Liberis; Petar Velickovic; Pietro Sormanni; Michele Vendruscolo; Pietro Liò (Bioinform., 2018)

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. - Damiano Piovesan; Francesco Tabaro; Lisanna Paladin; Marco Necci; Ivan Micetic; Carlo Camilloni; Norman E. Davey; Zsuzsanna Dosztányi; Bálint Mészáros; Alexander Miguel Monzon; Gustavo D. Parisi; Éva Schád; et al. (Nucleic Acids Res., 2018)

Sequence-based prediction of protein binding mode landscapes. - Attila Horvath; Márton Miskei; Viktor Ambrus; Michele Vendruscolo; Mónika Fuxreiter (PLoS Comput. Biol., 2020)

A kinetic ensemble of the Alzheimer's Aβ peptide. - Thomas Löhr; Kai Kohlhoff; Gabriella T. Heller; Carlo Camilloni; Michele Vendruscolo (Nat. Comput. Sci., 2021)

FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins. - András Hatos; Silvio C. E. Tosatto; Michele Vendruscolo; Mónika Fuxreiter (Nucleic Acids Res., 2022)

Sequence-based prediction of pH-dependent protein solubility using CamSol. - Marc Oeller; Ryan Kang; Rosie Bell; Hannes Ausserwöger; Pietro Sormanni; Michele Vendruscolo (Briefings Bioinform., 2023)

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; Alex S. Holehouse; Daniel A. Griffith; Ryan J. Emenecker; Ashwini Patil; Ronesh Sharma; Tatsuhiko Tsunoda; Alok Sharma; et al. (Nucleic Acids Res., 2023)

FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins. - András Hatos; João M. C. Teixeira; Susana Barrera-Vilarmau; Attila Horvath; Silvio C. E. Tosatto; Michele Vendruscolo; Mónika Fuxreiter (Nucleic Acids Res., 2023)

Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity. - Robert I. Horne; Jared Wilson-Godber; Alicia González Díaz; Z. Faidon Brotzakis; Srijit Seal; Rebecca C. Gregory; Andrea Possenti; Sean Chia; Michele Vendruscolo (J. Chem. Inf. Model., 2024)

Estimation of Ligand Binding Free Energy Using Multi-eGO. - Bruno Stegani; Emanuele Scalone; Fran Bacic Toplek; Thomas Löhr; Stefano Gianni; Michele Vendruscolo; Riccardo Capelli; Carlo Camilloni (J. Chem. Inf. Model., 2025)

Multi-state Protein Design with DynamicMPNN. - Alex Abrudan; Sebastian Pujalte Ojeda; Chaitanya K. Joshi; Matthew Greenig; Felipe Engelberger; Alena Khmelinskaia; Jens Meiler; Michele Vendruscolo; Tuomas P. J. Knowles (CoRR, 2025)