Pietro Sormanni

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Proteome-wide observation of the phenomenon of life on the edge of solubility

C. Dobson, F. Hartl, M. Vendruscolo, 2019, Proceedings of the National Academy of Sciences.

Parapred: antibody paratope prediction using convolutional and recurrent neural networks

Pietro Liò, Michele Vendruscolo, Petar Velickovic, 2018, Bioinform..

Sequence Analysis Parapred : Antibody Paratope Prediction using Convolutional and Recurrent Neural Networks

P. Lio’, Petar Velickovic, P. Sormanni, 2018 .

Paratope Prediction using Convolutional and Recurrent Neural Networks

P. Lio’, M. Vendruscolo, Petar Velickovic, 2017, bioRxiv.

Comparative Studies in the A30P and A53T α-Synuclein C. elegans Strains to Investigate the Molecular Origins of Parkinson's Disease

Romain F. Laine, J. B. Kirkegaard, C. Dobson, 2021, Frontiers in Cell and Developmental Biology.

Massively parallel C. elegans tracking provides multi-dimensional fingerprints for phenotypic discovery

Tuomas P. J. Knowles, Julius B. Kirkegaard, Michele Perni, 2018, Journal of Neuroscience Methods.

Delivery of Native Proteins into C. elegans Using a Transduction Protocol Based on Lipid Vesicles

C. Dobson, M. Vendruscolo, F. A. Aprile, 2017, Scientific Reports.

Third generation antibody discovery methods: in silico rational design.

Michele Vendruscolo, Pietro Sormanni, Francesco A Aprile, 2018, Chemical Society reviews.

Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics

Sarah A. Robinson, C. Deane, J. Warwicker, 2022, mAbs.

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins

Silvio C. E. Tosatto, Marco Necci, Damiano Piovesan, 2017, Nucleic Acids Res..

Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity

M. Bolognesi, M. Blackledge, D. de Sanctis, 2018, Nature Communications.

Different soluble aggregates of Aβ42 can give rise to cellular toxicity through different mechanisms

Michele Vendruscolo, Pietro Sormanni, Craig D. Hughes, 2019, Nature Communications.

Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability

M. Bolognesi, M. Vendruscolo, P. Sormanni, 2016, Scientific Reports.

The CamSol method of rational design of protein mutants with enhanced solubility.

Michele Vendruscolo, Pietro Sormanni, Francesco A Aprile, 2015, Journal of molecular biology.

Automated optimisation of solubility and conformational stability of antibodies and proteins

P. Sormanni, Nikolai Lorenzen, L. Sakhnini, 2022, bioRxiv.

Attentive cross-modal paratope prediction

Petar Velickovic, Andreea Deac, Pietro Sormanni, 2018, J. Comput. Biol..

Rapid and accurate in silico solubility screening of a monoclonal antibody library

Michele Vendruscolo, Pietro Sormanni, M. Vendruscolo, 2017, Scientific Reports.

A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data

Pietro Sormanni, Prajwal Ciryam, Ulrike A. Friedrich, 2018, bioRxiv.

Critical assessment of protein intrinsic disorder prediction

M. Y. Lobanov, David C. Jones, K. Paliwal, 2021, Nature Methods.

The s2D method: simultaneous sequence-based prediction of the statistical populations of ordered and disordered regions in proteins.

Piero Fariselli, Carlo Camilloni, Michele Vendruscolo, 2015, Journal of molecular biology.

π-Clamp-Mediated Homo- and Heterodimerization of Single-Domain Antibodies via Site-Specific Homobifunctional Conjugation

M. Vendruscolo, P. Sormanni, G. Bernardes, 2022, Journal of the American Chemical Society.

Approaches to expand the conventional toolbox for discovery and selection of antibodies with drug-like physicochemical properties

P. Sormanni, T. Menzen, P. Arosio, 2023, mAbs.

A rationally designed bicyclic peptide remodels Aβ42 aggregation in vitro and reduces its toxicity in a worm model of Alzheimer’s disease

C. Dobson, M. Vendruscolo, Gabriella T. Heller, 2020, Scientific Reports.

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming

C. Dobson, M. Vendruscolo, E. O’Brien, 2018, bioRxiv.

A Rationally Designed Hsp70 Variant Rescues the Aggregation-Associated Toxicity of Human IAPP in Cultured Pancreatic Islet β-Cells

M. Vendruscolo, F. A. Aprile, Marie N. Bongiovanni, 2018, International journal of molecular sciences.

A Rational Design Strategy for the Selective Activity Enhancement of a Molecular Chaperone toward a Target Substrate.

M. Vendruscolo, F. A. Aprile, Pietro Sormanni, 2015, Biochemistry.

A protein homeostasis signature in healthy brains recapitulates tissue vulnerability to Alzheimer’s disease

C. Dobson, M. Vendruscolo, Giulia Vecchi, 2016, Science Advances.

Quantifying misfolded protein oligomers as drug targets and biomarkers in Alzheimer and Parkinson diseases

M. Vendruscolo, J. Habchi, K. Kulenkampff, 2021, Nature Reviews Chemistry.

A natural product inhibits the initiation of α-synuclein aggregation and suppresses its toxicity

Michele Vendruscolo, Gabriella T Heller, Pietro Sormanni, 2017, Proceedings of the National Academy of Sciences.

Systematic Activity Maturation of a Single-Domain Antibody with Non-canonical Amino Acids through Chemical Mutagenesis

C. Dobson, M. Vendruscolo, P. Sormanni, 2020, Cell chemical biology.

Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes

R. Owens, M. Vendruscolo, D. Clare, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Rational design of a conformation-specific antibody for the quantification of Aβ oligomers

C. Dobson, M. Vendruscolo, Steven F. Lee, 2020, Proceedings of the National Academy of Sciences.

Selective targeting of primary and secondary nucleation pathways in Aβ42 aggregation using a rational antibody scanning method

Michele Vendruscolo, Sara Linse, Pietro Sormanni, 2017, Science Advances.

Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins

M. Vendruscolo, P. Sormanni, F. A. Aprile, 2015, Proceedings of the National Academy of Sciences.

Rationally Designed Bicyclic Peptides Prevent the Conversion of Aβ42 Assemblies Into Fibrillar Structures

M. Vendruscolo, F. A. Aprile, Tatsuya Ikenoue, 2021, Frontiers in Neuroscience.

Correction for Perni et al., A natural product inhibits the initiation of α-synuclein aggregation and suppresses its toxicity

J. B. Kirkegaard, C. Dobson, M. Vendruscolo, 2017, Proceedings of the National Academy of Sciences.

Neuroserpin and transthyretin are extracellular chaperones that preferentially inhibit amyloid formation

M. Vendruscolo, S. Satapathy, J. Buxbaum, 2021, Science advances.

MonteGrappa: An iterative Monte Carlo program to optimize biomolecular potentials in simplified models

Guido Tiana, Cristina Paissoni, Edith Heard, 2015, Comput. Phys. Commun..

Simultaneous quantification of protein order and disorder.

Sonia Longhi, Silvio C. E. Tosatto, A Keith Dunker, 2017, Nature chemical biology.

Targeting disordered proteins with small molecules using entropy.

Michele Vendruscolo, Gabriella T Heller, Pietro Sormanni, 2015, Trends in biochemical sciences.

Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates

Ulrike A. Friedrich, Naomi S. Altman, B. Bukau, 2020, bioRxiv.

Protein Solubility Predictions Using the CamSol Method in the Study of Protein Homeostasis.

M. Vendruscolo, P. Sormanni, Pietro Sormanni, 2019, Cold Spring Harbor perspectives in biology.

An antibody scanning method for the detection of α-synuclein oligomers in the serum of Parkinson's disease patients

D. Klenerman, M. Vendruscolo, C. Williams-Gray, 2022, Chemical science.

Sequence-based prediction of the solubility of peptides containing non-natural amino acids

M. Vendruscolo, L. De Maria, A. L. Gomes dos Santos, 2023, bioRxiv.

Sequence-based prediction of pH-dependent protein solubility using CamSol

M. Vendruscolo, Rosie Bell, Marc Oeller, 2023, Briefings Bioinform..

Sequence-based pH-dependent prediction of protein solubility using CamSol

M. Vendruscolo, P. Sormanni, Marc Oeller, 2022, bioRxiv.

Assessment of Therapeutic Antibody Developability by Combinations of In Vitro and In Silico Methods.

M. Vendruscolo, P. Sormanni, Nikolai Lorenzen, 2021, Methods in molecular biology.

Corneal Dystrophy Mutations Drive Pathogenesis by Targeting TGFBIp Stability and Solubility in a Latent Amyloid-forming Domain.

Nicholas P. Schafer, N. Schafer, D. Otzen, 2018, Journal of molecular biology.

Fibrillogenic propensity of the GroEL apical domain: A Janus‐faced minichaperone

M. Vendruscolo, K. Makabe, K. Kuwajima, 2012, FEBS letters.

Rationally Designed Antibodies as Research Tools to Study the Structure–Toxicity Relationship of Amyloid-β Oligomers

C. Dobson, M. Vendruscolo, F. Chiti, 2020, International journal of molecular sciences.

An open-source automated PEG precipitation assay to measure the relative solubility of proteins with low material requirement

M. Vendruscolo, P. Sormanni, Marc Oeller, 2021, Scientific Reports.

Oxetane Grafts Installed Site‐Selectively on Native Disulfides to Enhance Protein Stability and Activity In Vivo

Michele Vendruscolo, Pietro Sormanni, Michael J Deery, 2017, Angewandte Chemie.

Biochemical and biophysical comparison of human and mouse beta‐2 microglobulin reveals the molecular determinants of low amyloid propensity

P. Sormanni, C. Camilloni, R. Grandori, 2019, The FEBS journal.

Modulating the cardiotoxic behaviour of immunoglobulin light chain dimers through point mutations

M. Bolognesi, L. Diomede, G. Merlini, 2019, Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis.

In vitro and in silico assessment of the developability of a designed monoclonal antibody library

M. Vendruscolo, D. Otzen, L. De Maria, 2019, mAbs.

Inherent biophysical properties modulate the toxicity of soluble amyloidogenic light chains.

M. Bolognesi, R. Russo, M. Vendruscolo, 2019, Journal of molecular biology.

Supersaturated proteins are enriched at synapses and underlie cell and tissue vulnerability in Alzheimer's disease

C. Dobson, M. Vendruscolo, S. Rizzoli, 2019, Heliyon.

Delivery of Native Proteins into C. elegans Using a Transduction Protocol Based on Lipid Vesicles

C. Dobson, M. Vendruscolo, B. Mannini, 2017, Scientific Reports.

Editorial: Intrinsically Disordered Proteins and Regions: The Challenge to the Structure-Function Relationship

V. Uversky, P. Sormanni, C. Paissoni, 2022, Frontiers in Molecular Biosciences.

Discovery of Potent Inhibitors of α-Synuclein Aggregation Using Structure-Based Iterative Learning

B. Ghetti, M. Vendruscolo, B. Caughey, 2023, bioRxiv.

A method of predicting the in vitro fibril formation propensity of Aβ40 mutants based on their inclusion body levels in E. coli

M. Vendruscolo, S. Linse, A. Malmendal, 2019, Scientific Reports.

Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein

Carlo Camilloni, Michele Vendruscolo, Pietro Sormanni, 2014, Proceedings of the National Academy of Sciences.

An aggregation inhibitor specific to oligomeric intermediates of Aβ42 derived from phage display libraries of stable, small proteins

S. Linse, P. Sormanni, D. O’Connell, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Subdomain architecture and stability of a giant repeat protein.

M. Vendruscolo, L. Itzhaki, Maksym Tsytlonok, 2013, The journal of physical chemistry. B.

Understanding and controlling the molecular mechanisms of protein aggregation in mAb therapeutics.

Y. Ho, T. Michaels, K. Pang, 2023, Biotechnology advances.

Fragment-based computational design of antibodies targeting structured epitopes

R. Russo, J. Frydman, M. Vendruscolo, 2022, bioRxiv.

Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning

B. Ghetti, Ankit Srivastava, M. Vendruscolo, 2021, bioRxiv.

Critical assessment of protein intrinsic disorder prediction

Silvio C. E. Tosatto, Marco Necci, Damiano Piovesan, 2020, Nature Methods.

Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity

M. Bolognesi, M. Blackledge, D. de Sanctis, 2018, Nature Communications.

Conformational Entropy as a Potential Liability of Computationally Designed Antibodies

M. Vendruscolo, P. Sormanni, Thomas Löhr, 2022, Biomolecules.

Multidimensional Protein Solubility Optimization with an Ultrahigh-Throughput Microfluidic Platform

M. Vendruscolo, P. Sormanni, A. Levin, 2022, bioRxiv.

AbNatiV: VQ-VAE-based assessment of antibody and nanobody nativeness for engineering, selection, and computational design

M. Greenig, Kieran Didi, Pietro Sormanni, 2023 .

A method of predicting the in vitro fibril formation propensity of Aβ40 mutants based on their inclusion body levels in E. coli

M. Vendruscolo, S. Linse, A. Malmendal, 2019, Scientific Reports.

Computational maturation of a single-domain antibody against Aβ42 aggregation

M. Vendruscolo, P. Sormanni, Jiacheng Lin, 2021, Chemical science.

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

Silvio C. E. Tosatto, M. Y. Lobanov, Md. Wasi Ul Kabir, 2023, Nucleic Acids Res..

AbNatiV: VQ-VAE-based assessment of antibody and nanobody nativeness for hit selection, humanisation, and engineering

Kieran Didi, Pietro Sormanni, Aubin Ramon, 2023, bioRxiv.

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming

C. Dobson, M. Vendruscolo, E. O’Brien, 2018, Scientific Reports.

Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning

B. Ghetti, M. Vendruscolo, J. Habchi, 2021, bioRxiv.

Attentive cross-modal paratope prediction

Petar Velickovic, Andreea Deac, Pietro Sormanni, 2018, J. Comput. Biol..

Rational design of a conformation-specific antibody for the quantification of Aβ oligomers

C. Dobson, M. Vendruscolo, Steven F. Lee, 2020, Proceedings of the National Academy of Sciences.

Sequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids

Werngard Czechtizky, Marc Oeller, P. Zlatoidský, 2023, Nature communications.