List of works - Silvio C.E. Tosatto

2mit, an intronic gene of Drosophila melanogaster timeless2, is involved in behavioral plasticity.

scientific article

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

scientific article published in 2022

A Novel Missense Variant in MYL2 Gene Associated with Hypertrophic Cardiomyopathy Showing High Incidence of Restrictive Physiology

scientific article published on 31 January 2020

A STRP-ed definition of Structured Tandem Repeats in Proteins

scientific article published in December 2023

A comprehensive assessment of long intrinsic protein disorder from the DisProt database.

scientific article published on 18 September 2017

A computational model of the LGI1 protein suggests a common binding site for ADAM proteins.

scientific article

A targeted next-generation gene panel reveals a novel heterozygous nonsense variant in the TP63 gene in patients with arrhythmogenic cardiomyopathy

scientific article published on 17 November 2018

APICURON: a database to credit and acknowledge the work of biocurators

Adding structural information to the von Hippel-Lindau (VHL) tumor suppressor interaction network.

scientific article published on 28 October 2009

Align: a C++ class library and web server for rapid sequence alignment prototyping.

scientific article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database.

scientific article

Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation.

scientific article published in April 2005

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

scientific article published on 03 September 2019

Assessing predictors for new post translational modification sites: A case study on hydroxylation

scientific article published on 22 June 2020

Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge

scientific article published on 03 July 2019

BOOGIE: Predicting Blood Groups from High Throughput Sequencing Data.

scientific article

Bluues server: electrostatic properties of wild-type and mutated protein structures.

scientific article

CDKN2A unclassified variants in familial malignant melanoma: combining functional and computational approaches for their assessment.

scientific article published on 21 May 2014

Ca2+ binding to F-ATP synthase β subunit triggers the mitochondrial permeability transition

scientific article published on 15 May 2017

Cardiomyopathy in patients with POMT1-related congenital and limb-girdle muscular dystrophy.

scientific article

Characterization of intellectual disability and autism comorbidity through gene panel sequencing

scientific article published on 02 August 2019

Comparison of protein repeat classifications based on structure and sequence families

scientific article

Comprehensive large-scale assessment of intrinsic protein disorder

scientific article published on 21 September 2014

Computational analysis of prolyl hydroxylase domain-containing protein 2 (PHD2) mutations promoting polycythemia insurgence in humans.

scientific article published on 12 January 2016

Conformational diversity analysis reveals three functional mechanisms in proteins

scientific article

Correct machine learning on protein sequences: a peer-reviewing perspective.

scientific article

Crohn disease risk prediction-Best practices and pitfalls with exome data.

scientific article

Decomposing protein networks into domain-domain interactions.

scientific article published in September 2005

Design and analysis of a Petri net model of the Von Hippel-Lindau (VHL) tumor suppressor interaction network

scientific article

DisProt 7.0: a major update of the database of disordered proteins.

scientific article

Disorder transitions and conformational diversity cooperatively modulate biological function in proteins.

scientific article published on 02 April 2016

Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family

scientific article published on 28 July 2017

Electric dipole reorientation in the interaction of botulinum neurotoxins with neuronal membranes

scientific article published on 02 July 2009

Ensembles from ordered and disordered proteins reveal similar structural constraints during evolution

Evaluation of the steric impact of flavin adenine dinucleotide in Drosophila melanogaster cryptochrome function.

scientific article published on 12 July 2014

Evolutionary and structural insights into the multifaceted glutathione peroxidase (Gpx) superfamily.

scientific article

Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank

scientific article published on 24 June 2020

FELLS: fast estimator of latent local structure.

scientific article

Familial temporal lobe epilepsy with psychic auras associated with a novel LGI1 mutation.

scientific article published in March 2011

Fine-Grained Statistical Torsion Angle Potentials are Effective in Discriminating Native Protein Structures

scientific article published on 01 March 2006

Functional insights from the structural modelling of a small Fe-hydrogenase

scientific article published on 10 November 2005

Functional interaction of phospholipid hydroperoxide glutathione peroxidase with sperm mitochondrion-associated cysteine-rich protein discloses the adjacent cysteine motif as a new substrate of the selenoperoxidase.

scientific article

FuzDB: a new phase in understanding fuzzy interactions

scientific article published on 01 January 2022

Gamma-glutamyl transferase in the cell wall participates in extracellular glutathione salvage from the root apoplast.

scientific article

Genotype-phenotype relations of the von Hippel-Lindau tumor suppressor inferred from a large-scale analysis of disease mutations and interactors

scientific article published on 03 April 2019

Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust.

scientific article

Heterozygous reelin mutations cause autosomal-dominant lateral temporal epilepsy

scientific article published on June 2015

INGA 2.0: improving protein function prediction for the dark proteome

scientific article published on 01 July 2019

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.

scientific article published on 27 May 2015

Improving the quality of protein structure models by selecting from alignment alternatives

scientific article

Inhibitory interaction of the 14-3-3 proteins with ubiquitous (PMCA1) and tissue-specific (PMCA3) isoforms of the plasma membrane Ca2+ pump

scientific journal article

Insights into the proline hydroxylase (PHD) family, molecular evolution and its impact on human health.

scientific article

InterPro in 2017-beyond protein family and domain annotations

scientific article

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

article by Alex Mitchell et al published 6 November 2018 in Nucleic Acids Research

LGI1 mutations in autosomal dominant and sporadic lateral temporal epilepsy.

scientific article published on April 2009

Large-scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe

scientific article

Large-scale prediction of protein structure and function from sequence.

scientific article

Looking for putative phenoloxidases of compound ascidians: Haemocyanin-like proteins in Polyandrocarpa misakiensis and Botryllus schlosseri

scientific article published on 12 June 2012

Low density lipoprotein misfolding and amyloidogenesis.

scientific article

MOBI: a web server to define and visualize structural mobility in NMR protein ensembles.

scientific article

Mapping pathogenic mutations suggests an innovative structural model for the pendrin (SLC26A4) transmembrane domain.

scientific article published on 19 October 2016

Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures.

scientific article published on 18 September 2017

MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins

scientific article

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

scientific article published on 10 November 2017

MobiDB: a comprehensive database of intrinsic protein disorder annotations.

scientific article

Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models

scientific article published in 2022

Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes

scientific article published on 04 July 2019

Neurocognitive assessment and DNA sequencing expand the phenotype and genotype spectrum of Alström syndrome

scientific article published on 07 January 2021

PANADA: protein association network annotation, determination and analysis.

scientific article

PASTA 2.0: an improved server for protein aggregation prediction

scientific article

Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5

scientific article published on 17 August 2019

Protein function prediction using guilty by association from interaction networks.

scientific article published on 28 July 2015

QMEAN: A comprehensive scoring function for model quality assessment.

scientific article

QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information.

scientific article

REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform.

scientific article published on June 2009

RING: networking interacting residues, evolutionary information and energetics in protein structures.

scientific article

RUBI: rapid proteomic-scale prediction of lysine ubiquitination and factors influencing predictor performance.

scientific article published on 23 December 2013

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures.

scientific article

RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.

scientific article published in July 2018

RepeatsDB: a database of tandem repeat protein structures

scientific article (publication date: 5 December 2013)

SODA: prediction of protein solubility from disorder and aggregation propensity.

scientific article published on 13 May 2017

Secretion-Positive LGI1 Mutations Linked to Lateral Temporal Epilepsy Impair Binding to ADAM22 and ADAM23 Receptors

scientific article

Structural in silico dissection of the collagen V interactome to identify genotype-phenotype correlations in classic Ehlers-Danlos Syndrome (EDS)

scientific article published on 19 November 2015

Structural protein reorganization and fold emergence investigated through amino acid sequence permutations

scientific article published on 21 October 2014

TAP score: torsion angle propensity normalization applied to local protein structure evaluation.

scientific article

TESE: generating specific protein structure test set ensembles.

scientific article

The Ca 2+ regulatory site of the permeability transition pore is within the catalytic core of F-ATP synthase

The Feature Viewer: A visualization tool for positional annotations on a sequence

scientific article published on 27 January 2020

The Gene Ontology knowledgebase in 2023

scientific article published in 2023

The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes

scientific article published on 29 October 2020

The N-terminal half of the receptor domain of botulinum neurotoxin A binds to microdomains of the plasma membrane

scientific article published on 20 January 2009

The PASTA server for protein aggregation prediction.

scientific article published on 24 August 2007

The RING 2.0 web server for high quality residue interaction networks

scientific article

The SSEA server for protein secondary structure alignment.

scientific article

The catalytic site of glutathione peroxidases.

scientific article published in September 2008

The role of the N-terminal tail for the oligomerization, folding and stability of human frataxin

scientific article published on 24 July 2013

The thioredoxin specificity of Drosophila GPx: a paradigm for a peroxiredoxin-like mechanism of many glutathione peroxidases.

scientific article published on 13 October 2006

The victor/FRST function for model quality estimation.

scientific article

Unfoldome variation upon plant-pathogen interactions: strawberry infection by Colletotrichum acutatum

scientific article published on 6 August 2015

VHLdb: A database of von Hippel-Lindau protein interactors and mutations

scientific article published on 11 August 2016

Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins

scientific article published on 01 January 2018

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

scientific article published on 21 June 2017

List of works by Silvio C.E. Tosatto

2mit, an intronic gene of Drosophila melanogaster timeless2, is involved in behavioral plasticity.

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

A Novel Missense Variant in MYL2 Gene Associated with Hypertrophic Cardiomyopathy Showing High Incidence of Restrictive Physiology

A STRP-ed definition of Structured Tandem Repeats in Proteins

A comprehensive assessment of long intrinsic protein disorder from the DisProt database.

A computational model of the LGI1 protein suggests a common binding site for ADAM proteins.

A targeted next-generation gene panel reveals a novel heterozygous nonsense variant in the TP63 gene in patients with arrhythmogenic cardiomyopathy

APICURON: a database to credit and acknowledge the work of biocurators

Adding structural information to the von Hippel-Lindau (VHL) tumor suppressor interaction network.

Align: a C++ class library and web server for rapid sequence alignment prototyping.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database.

Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation.

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

Assessing predictors for new post translational modification sites: A case study on hydroxylation

Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge

BOOGIE: Predicting Blood Groups from High Throughput Sequencing Data.

Bluues server: electrostatic properties of wild-type and mutated protein structures.

CDKN2A unclassified variants in familial malignant melanoma: combining functional and computational approaches for their assessment.

Ca2+ binding to F-ATP synthase β subunit triggers the mitochondrial permeability transition

Cardiomyopathy in patients with POMT1-related congenital and limb-girdle muscular dystrophy.

Characterization of intellectual disability and autism comorbidity through gene panel sequencing

Comparison of protein repeat classifications based on structure and sequence families

Comprehensive large-scale assessment of intrinsic protein disorder

Computational analysis of prolyl hydroxylase domain-containing protein 2 (PHD2) mutations promoting polycythemia insurgence in humans.

Conformational diversity analysis reveals three functional mechanisms in proteins

Correct machine learning on protein sequences: a peer-reviewing perspective.

Crohn disease risk prediction-Best practices and pitfalls with exome data.

Decomposing protein networks into domain-domain interactions.

Design and analysis of a Petri net model of the Von Hippel-Lindau (VHL) tumor suppressor interaction network

DisProt 7.0: a major update of the database of disordered proteins.

Disorder transitions and conformational diversity cooperatively modulate biological function in proteins.

Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family

Electric dipole reorientation in the interaction of botulinum neurotoxins with neuronal membranes

Ensembles from ordered and disordered proteins reveal similar structural constraints during evolution

Evaluation of the steric impact of flavin adenine dinucleotide in Drosophila melanogaster cryptochrome function.

Evolutionary and structural insights into the multifaceted glutathione peroxidase (Gpx) superfamily.

Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank

FELLS: fast estimator of latent local structure.

Familial temporal lobe epilepsy with psychic auras associated with a novel LGI1 mutation.

Fine-Grained Statistical Torsion Angle Potentials are Effective in Discriminating Native Protein Structures

Functional insights from the structural modelling of a small Fe-hydrogenase

Functional interaction of phospholipid hydroperoxide glutathione peroxidase with sperm mitochondrion-associated cysteine-rich protein discloses the adjacent cysteine motif as a new substrate of the selenoperoxidase.

FuzDB: a new phase in understanding fuzzy interactions

Gamma-glutamyl transferase in the cell wall participates in extracellular glutathione salvage from the root apoplast.

Genotype-phenotype relations of the von Hippel-Lindau tumor suppressor inferred from a large-scale analysis of disease mutations and interactors

Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust.

Heterozygous reelin mutations cause autosomal-dominant lateral temporal epilepsy

INGA 2.0: improving protein function prediction for the dark proteome

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.

Improving the quality of protein structure models by selecting from alignment alternatives

Inhibitory interaction of the 14-3-3 proteins with ubiquitous (PMCA1) and tissue-specific (PMCA3) isoforms of the plasma membrane Ca2+ pump

Insights into the proline hydroxylase (PHD) family, molecular evolution and its impact on human health.

InterPro in 2017-beyond protein family and domain annotations

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

LGI1 mutations in autosomal dominant and sporadic lateral temporal epilepsy.

Large-scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe

Large-scale prediction of protein structure and function from sequence.

Looking for putative phenoloxidases of compound ascidians: Haemocyanin-like proteins in Polyandrocarpa misakiensis and Botryllus schlosseri

Low density lipoprotein misfolding and amyloidogenesis.

MOBI: a web server to define and visualize structural mobility in NMR protein ensembles.

Mapping pathogenic mutations suggests an innovative structural model for the pendrin (SLC26A4) transmembrane domain.

Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures.

MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins

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

MobiDB: a comprehensive database of intrinsic protein disorder annotations.

Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models

Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes

Neurocognitive assessment and DNA sequencing expand the phenotype and genotype spectrum of Alström syndrome

PANADA: protein association network annotation, determination and analysis.

PASTA 2.0: an improved server for protein aggregation prediction

Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5

Protein function prediction using guilty by association from interaction networks.

QMEAN: A comprehensive scoring function for model quality assessment.

QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information.

REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform.

RING: networking interacting residues, evolutionary information and energetics in protein structures.

RUBI: rapid proteomic-scale prediction of lysine ubiquitination and factors influencing predictor performance.

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures.