Michele Vendruscolo

23 papers Journal 22Unranked 1

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings. CoRR Josef Hanke, Sebastian Pujalte Ojeda, Shengyu Zhang, Werngard Czechtizky, Leonardo De Maria, Michele Vendruscolo
2025	J	`jnl`	Estimation of Ligand Binding Free Energy Using Multi-eGO. J. Chem. Inf. Model. Bruno Stegani, Emanuele Scalone, Fran Bacic Toplek, Thomas Löhr, Stefano Gianni, Michele Vendruscolo, Riccardo Capelli, Carlo Camilloni
2025	J	`jnl`	Multi-state Protein Design with DynamicMPNN. CoRR Alex Abrudan, Sebastian Pujalte Ojeda, Chaitanya K. Joshi, Matthew Greenig, Felipe Engelberger, Alena Khmelinskaia, Jens Meiler, Michele Vendruscolo, Tuomas P. J. Knowles
2025	J	`jnl`	Proteostasis signatures in human diseases. PLoS Comput. Biol. Christine M. Lim, Michele Vendruscolo
2024	J	`jnl`	Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity. J. Chem. Inf. Model. Robert I. Horne, Jared Wilson-Godber, Alicia González Díaz, Z. Faidon Brotzakis, Srijit Seal, Rebecca C. Gregory, Andrea Possenti, Sean Chia, Michele Vendruscolo
2023	J	`jnl`	CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 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, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan
2023	J	`jnl`	FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins. Nucleic Acids Res. András Hatos, João M. C. Teixeira, Susana Barrera-Vilarmau, Attila Horvath, Silvio C. E. Tosatto, Michele Vendruscolo, Mónika Fuxreiter
2023	J	`jnl`	Sequence-based prediction of pH-dependent protein solubility using CamSol. Briefings Bioinform. Marc Oeller, Ryan Kang, Rosie Bell, Hannes Ausserwöger, Pietro Sormanni, Michele Vendruscolo
2022	J	`jnl`	FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins. Nucleic Acids Res. András Hatos, Silvio C. E. Tosatto, Michele Vendruscolo, Mónika Fuxreiter
2021	J	`jnl`	A kinetic ensemble of the Alzheimer's Aβ peptide. Nat. Comput. Sci. Thomas Löhr, Kai Kohlhoff, Gabriella T. Heller, Carlo Camilloni, Michele Vendruscolo
2020	J	`jnl`	Sequence-based prediction of protein binding mode landscapes. PLoS Comput. Biol. Attila Horvath, Márton Miskei, Viktor Ambrus, Michele Vendruscolo, Mónika Fuxreiter
2018	J	`jnl`	MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Res. 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, Pietro Sormanni, Peter Tompa, Michele Vendruscolo, Wim F. Vranken, Silvio C. E. Tosatto
2018	J	`jnl`	Parapred: antibody paratope prediction using convolutional and recurrent neural networks. Bioinform. Edgar Liberis, Petar Velickovic, Pietro Sormanni, Michele Vendruscolo, Pietro Liò
2015	J	`jnl`	Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations. PLoS Comput. Biol. Predrag Kukic, Arvind Kannan, Maurits J. J. Dijkstra, Sanne Abeln, Carlo Camilloni, Michele Vendruscolo
2014	J	`jnl`	ALMOST: An all atom molecular simulation toolkit for protein structure determination. J. Comput. Chem. Biao Fu, Aleksandr B. Sahakyan, Carlo Camilloni, Gian Gaetano Tartaglia, Emanuele Paci, Amedeo Caflisch, Michele Vendruscolo, Andrea Cavalli
2014	J	`jnl`	pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. Nucleic Acids Res. 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, Vladimir N. Uversky, Michele Vendruscolo, David S. Wishart, Peter E. Wright, Peter Tompa
2011	J	`jnl`	Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation. PLoS Comput. Biol. Anthony W. Fitzpatrick, Tuomas P. J. Knowles, Christopher A. Waudby, Michele Vendruscolo, Christopher M. Dobson
2009	J	`jnl`	A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation. PLoS Comput. Biol. Stefan Auer, Antonio Trovato, Michele Vendruscolo
2008	J	`jnl`	A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates. PLoS Comput. Biol. Stefan Auer, Filip Meersman, Christopher M. Dobson, Michele Vendruscolo
2008	J	`jnl`	Competition between protein aggregation and protein complex formation. BMC Bioinform. Sebastian Pechmann, Emmanuel D. Levy, Gian Gaetano Tartaglia, Michele Vendruscolo
2008	J	`jnl`	Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms. PLoS Comput. Biol. Tammy M. K. Cheng, Yu-En Lu, Michele Vendruscolo, Pietro Liò, Tom L. Blundell
2007	J	`jnl`	Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils. PLoS Comput. Biol. Mookyung Cheon, Iksoo Chang, Sandipan Mohanty, Leila M. Luheshi, Christopher M. Dobson, Michele Vendruscolo, Giorgio Favrin
2002	—	`conf`	Protein folding using inter-residue contacts. 3DPVT Michele Vendruscolo