Silvio C E Tosatto

Silvio C E Tosatto

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Silvio C E Tosatto

Silvio C E Tosatto

Publications by authors named "Silvio C E Tosatto"

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Insights into the molecular features of the von Hippel-Lindau-like protein.

Amino Acids 2019 Nov 4;51(10-12):1461-1474. Epub 2019 Sep 4.

Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padua, Italy.

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http://dx.doi.org/10.1007/s00726-019-02781-8DOI Listing
November 2019

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Authors:
Naihui Zhou Yuxiang Jiang Timothy R Bergquist Alexandra J Lee Balint Z Kacsoh Alex W Crocker Kimberley A Lewis George Georghiou Huy N Nguyen Md Nafiz Hamid Larry Davis Tunca Dogan Volkan Atalay Ahmet S Rifaioglu Alperen Dalkıran Rengul Cetin Atalay Chengxin Zhang Rebecca L Hurto Peter L Freddolino Yang Zhang Prajwal Bhat Fran Supek José M Fernández Branislava Gemovic Vladimir R Perovic Radoslav S Davidović Neven Sumonja Nevena Veljkovic Ehsaneddin Asgari Mohammad R K Mofrad Giuseppe Profiti Castrense Savojardo Pier Luigi Martelli Rita Casadio Florian Boecker Heiko Schoof Indika Kahanda Natalie Thurlby Alice C McHardy Alexandre Renaux Rabie Saidi Julian Gough Alex A Freitas Magdalena Antczak Fabio Fabris Mark N Wass Jie Hou Jianlin Cheng Zheng Wang Alfonso E Romero Alberto Paccanaro Haixuan Yang Tatyana Goldberg Chenguang Zhao Liisa Holm Petri Törönen Alan J Medlar Elaine Zosa Itamar Borukhov Ilya Novikov Angela Wilkins Olivier Lichtarge Po-Han Chi Wei-Cheng Tseng Michal Linial Peter W Rose Christophe Dessimoz Vedrana Vidulin Saso Dzeroski Ian Sillitoe Sayoni Das Jonathan Gill Lees David T Jones Cen Wan Domenico Cozzetto Rui Fa Mateo Torres Alex Warwick Vesztrocy Jose Manuel Rodriguez Michael L Tress Marco Frasca Marco Notaro Giuliano Grossi Alessandro Petrini Matteo Re Giorgio Valentini Marco Mesiti Daniel B Roche Jonas Reeb David W Ritchie Sabeur Aridhi Seyed Ziaeddin Alborzi Marie-Dominique Devignes Da Chen Emily Koo Richard Bonneau Vladimir Gligorijević Meet Barot Hai Fang Stefano Toppo Enrico Lavezzo Marco Falda Michele Berselli Silvio C E Tosatto Marco Carraro Damiano Piovesan Hafeez Ur Rehman Qizhong Mao Shanshan Zhang Slobodan Vucetic Gage S Black Dane Jo Erica Suh Jonathan B Dayton Dallas J Larsen Ashton R Omdahl Liam J McGuffin Danielle A Brackenridge Patricia C Babbitt Jeffrey M Yunes Paolo Fontana Feng Zhang Shanfeng Zhu Ronghui You Zihan Zhang Suyang Dai Shuwei Yao Weidong Tian Renzhi Cao Caleb Chandler Miguel Amezola Devon Johnson Jia-Ming Chang Wen-Hung Liao Yi-Wei Liu Stefano Pascarelli Yotam Frank Robert Hoehndorf Maxat Kulmanov Imane Boudellioua Gianfranco Politano Stefano Di Carlo Alfredo Benso Kai Hakala Filip Ginter Farrokh Mehryary Suwisa Kaewphan Jari Björne Hans Moen Martti E E Tolvanen Tapio Salakoski Daisuke Kihara Aashish Jain Tomislav Šmuc Adrian Altenhoff Asa Ben-Hur Burkhard Rost Steven E Brenner Christine A Orengo Constance J Jeffery Giovanni Bosco Deborah A Hogan Maria J Martin Claire O'Donovan Sean D Mooney Casey S Greene Predrag Radivojac Iddo Friedberg

Genome Biol 2019 11 19;20(1):244. Epub 2019 Nov 19.

Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.

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http://dx.doi.org/10.1186/s13059-019-1835-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864930PMC
November 2019

PhaSePro: the database of proteins driving liquid-liquid phase separation.

Nucleic Acids Res 2019 Oct 15. Epub 2019 Oct 15.

Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.

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http://dx.doi.org/10.1093/nar/gkz848DOI Listing
October 2019

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

Eur Biophys J 2019 Sep 4;48(6):559-568. Epub 2019 Jul 4.

Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina.

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http://dx.doi.org/10.1007/s00249-019-01384-1DOI Listing
September 2019

INGA 2.0: improving protein function prediction for the dark proteome.

Nucleic Acids Res 2019 Jul;47(W1):W373-W378

Department of Biomedical Sciences, University of Padua, Padua, Italy.

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http://dx.doi.org/10.1093/nar/gkz375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602455PMC
July 2019

Ensembles from Ordered and Disordered Proteins Reveal Similar Structural Constraints during Evolution.

J Mol Biol 2019 Mar 5;431(6):1298-1307. Epub 2019 Feb 5.

Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina.

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http://dx.doi.org/10.1016/j.jmb.2019.01.031DOI Listing
March 2019

Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases.

Front Physiol 2019 27;10:314. Epub 2019 Mar 27.

Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.3389/fphys.2019.00314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445884PMC
March 2019

The clinical spectrum of -related myopathy.

Neurology 2018 10 26;91(17):e1629-e1641. Epub 2018 Sep 26.

From the Neuromuscular Center (C.S., C.B., L.B., B.P., F.G., S.V., B.F.G., G.S., E.P.), Department of Neurosciences, and Departments of Cardiac, Thoracic and Vascular Sciences (M.P., C.C.), Biomedical Sciences (G.M., S.C.E.T.), and Medicine (R.S.), Section of Radiology, University of Padova, Italy; Dubowitz Neuromuscular Centre (Developmental Neuroscience Programme) (F.C.), UCL Great Ormond Street Institute of Child Health, University College London, UK; Neuromuscular and Rare Disease Unit (I.C., M.M.), Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan; Department of Biomedical and Neuromotor Sciences (G.C., V.P.), University of Bologna; and CNR Institute of Neuroscience (S.C.E.T.), Padova, Italy.

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http://dx.doi.org/10.1212/WNL.0000000000006387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205688PMC
October 2018

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

Nucleic Acids Res 2018 07;46(W1):W402-W407

Dept. of Biomedical Sciences, University of Padua, Padua, Italy.

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http://dx.doi.org/10.1093/nar/gky360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031040PMC
July 2018

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

Bioinformatics 2018 02;34(3):445-452

Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btx590DOI Listing
February 2018

Classification of β-hairpin repeat proteins.

J Struct Biol 2018 02 7;201(2):130-138. Epub 2017 Oct 7.

Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, Montpellier 34293, France; Institut de Biologie Computationnelle, Montpellier, France. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2017.10.001DOI Listing
February 2018

Editorial for special issue "Proteins with tandem repeats: sequences, structures and functions"☆.

J Struct Biol 2018 02 30;201(2):86-87. Epub 2017 Dec 30.

Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy; CNR Institute of Neuroscience, I-35121 Padova, Italy.

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http://dx.doi.org/10.1016/j.jsb.2017.12.011DOI Listing
February 2018

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

Bioinformatics 2018 01;34(1):122-123

Department of Biomedical Sciences, University of Padua Viale G. Colombo 3, Padova 35121, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btx592DOI Listing
January 2018

CNTNAP2 mutations and autosomal dominant epilepsy with auditory features.

Epilepsy Res 2018 01 21;139:51-53. Epub 2017 Nov 21.

CNR-Neuroscience Institute, Section of Padua, Padova, Italy; Department of Biomedical Sciences, University of Padua, Padova, Italy. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09201211173044
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http://dx.doi.org/10.1016/j.eplepsyres.2017.11.006DOI Listing
January 2018

PhytoTypeDB: a database of plant protein inter-cultivar variability and function.

Database (Oxford) 2018 01 1;2018. Epub 2018 Jan 1.

Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, Padua, Italy.

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http://dx.doi.org/10.1093/database/bay125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301341PMC
January 2018

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

Database (Oxford) 2018 01 1;2018. Epub 2018 Jan 1.

Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58b, Padua, Italy.

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http://dx.doi.org/10.1093/database/bay127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301333PMC
January 2018

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

Hum Mutat 2017 09 21;38(9):1193-1200. Epub 2017 Mar 21.

Department of Woman and Child Health, University of Padova, Padova, Italy.

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http://dx.doi.org/10.1002/humu.23177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5509518PMC
September 2017

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

Nucleic Acids Res 2017 07;45(W1):W236-W240

Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121 Padova, Italy.

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http://dx.doi.org/10.1093/nar/gkx412DOI Listing
July 2017

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

Sci Rep 2017 07 28;7(1):6829. Epub 2017 Jul 28.

Molecular Genetics of Neurodevelopmental disorders, Department of Woman and Child Health, University of Padua, Padua, Italy.

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http://dx.doi.org/10.1038/s41598-017-05748-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533708PMC
July 2017

FELLS: fast estimator of latent local structure.

Bioinformatics 2017 Jun;33(12):1889-1891

Department of Biomedical Sciences, University of Padua, Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btx085DOI Listing
June 2017

MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins.

Bioinformatics 2017 05;33(9):1402-1404

Department of Biomedical Sciences, University of Padua, 35121 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btx015DOI Listing
May 2017

Novel interactions of the von Hippel-Lindau (pVHL) tumor suppressor with the CDKN1 family of cell cycle inhibitors.

Sci Rep 2017 04 20;7:46562. Epub 2017 Apr 20.

Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padova, Italy.

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http://dx.doi.org/10.1038/srep46562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397843PMC
April 2017

Conformational diversity analysis reveals three functional mechanisms in proteins.

PLoS Comput Biol 2017 02 13;13(2):e1005398. Epub 2017 Feb 13.

Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina.

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http://dx.doi.org/10.1371/journal.pcbi.1005398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330503PMC
February 2017

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

Biochimie 2017 Jan 19;132:109-120. Epub 2016 Oct 19.

Dept. of Biomedical Sciences, CRIBI Biotechnology Center, University of Padua, Italy; CNR Institute of Neuroscience, Padua, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.biochi.2016.10.002DOI Listing
January 2017

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

Nucleic Acids Res 2017 01 29;45(D1):D308-D312. Epub 2016 Nov 29.

Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy

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http://dx.doi.org/10.1093/nar/gkw1136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210593PMC
January 2017

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

Protein Sci 2016 12 25;25(12):2164-2174. Epub 2016 Oct 25.

Department of Biomedical Sciences and CRIBI Biotech Center, University of Padua, Padua, Italy.

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http://dx.doi.org/10.1002/pro.3041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119570PMC
December 2016

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

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

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

Sci Rep 2016 08 11;6:31128. Epub 2016 Aug 11.

Department of Biomedical Sciences and CRIBI Biotechnology Center, University of Padova, Viale G. Colombo 3, 35121, Padova, Italy.

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http://dx.doi.org/10.1038/srep31128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980628PMC
August 2016

The RING 2.0 web server for high quality residue interaction networks.

Nucleic Acids Res 2016 07 19;44(W1):W367-74. Epub 2016 May 19.

Department of Biomedical Sciences, University of Padua, Padua 35121, Italy CNR Institute of Neuroscience, Padua 35121, Italy

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http://dx.doi.org/10.1093/nar/gkw315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987896PMC
July 2016

Identification of repetitive units in protein structures with ReUPred.

Amino Acids 2016 06 22;48(6):1391-400. Epub 2016 Feb 22.

Department of Biomedical Sciences, University of Padua, Padua, Italy.

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http://dx.doi.org/10.1007/s00726-016-2187-2DOI Listing
June 2016

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

Protein Sci 2016 06 18;25(6):1138-46. Epub 2016 Apr 18.

Structural Bioinformatics Group, Department of Science and Technology, National University of Quilmes, Argentina.

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http://dx.doi.org/10.1002/pro.2931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941770PMC
June 2016

BOOGIE: Predicting Blood Groups from High Throughput Sequencing Data.

PLoS One 2015 20;10(4):e0124579. Epub 2015 Apr 20.

Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124579PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404330PMC
January 2016

Tools and data services registry: a community effort to document bioinformatics resources.

Nucleic Acids Res 2016 Jan 3;44(D1):D38-47. Epub 2015 Nov 3.

Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1093/nar/gkv1116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702812PMC
January 2016

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

Sci Rep 2016 Jan 12;6:18716. Epub 2016 Jan 12.

Department of Biomedical Sciences and CRIBI Biotechnology Center, University of Padova, Viale G. Colombo 3, 35121, Padova, Italy.

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http://www.nature.com/articles/srep18716
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http://dx.doi.org/10.1038/srep18716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709589PMC
January 2016

Protein function prediction using guilty by association from interaction networks.

Amino Acids 2015 Dec 28;47(12):2583-92. Epub 2015 Jul 28.

Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131, Padua, Italy.

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http://dx.doi.org/10.1007/s00726-015-2049-3DOI Listing
December 2015

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

FEBS Lett 2015 Dec 19;589(24 Pt B):3871-8. Epub 2015 Nov 19.

Department of Biomedical Sciences and CRIBI Biotechnology Center, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.febslet.2015.11.022DOI Listing
December 2015

Comparison of protein repeat classifications based on structure and sequence families.

Biochem Soc Trans 2015 Oct;43(5):832-7

Department of Biomedical Sciences, University of Padua, viale G. Colombo 3, 35121 Padova, Italy

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http://dx.doi.org/10.1042/BST20150079DOI Listing
October 2015

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

Biochimie 2015 Sep 15;116:114-24. Epub 2015 Jul 15.

Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121, Padova, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.biochi.2015.07.009DOI Listing
September 2015

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

Plant Mol Biol 2015 Sep 6;89(1-2):49-65. Epub 2015 Aug 6.

Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1007/s11103-015-0353-7DOI Listing
September 2015

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

Nucleic Acids Res 2015 Jul 27;43(W1):W134-40. Epub 2015 May 27.

Department of Biomedical Sciences, University of Padua, Padua 35121, Italy CNR Institute of Neuroscience, Padua 35121, Italy

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http://dx.doi.org/10.1093/nar/gkv523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489281PMC
July 2015

Isoform-specific interactions of the von Hippel-Lindau tumor suppressor protein.

Sci Rep 2015 Jul 27;5:12605. Epub 2015 Jul 27.

1] Department of Biomedical Sciences, University of Padova [2] CNR Institute of Neuroscience, Padova, Italy.

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http://dx.doi.org/10.1038/srep12605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515828PMC
July 2015

The Victor C++ library for protein representation and advanced manipulation.

Bioinformatics 2015 Apr 19;31(7):1138-40. Epub 2014 Nov 19.

Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btu773DOI Listing
April 2015

Comprehensive large-scale assessment of intrinsic protein disorder.

Bioinformatics 2015 Jan 21;31(2):201-8. Epub 2014 Sep 21.

Department of Biomedical Sciences, Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy and Institute for Advanced Simulation, Forschungszentrum Juelich, Wilhelm-Johnen-Str., 52425 Juelich, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btu625DOI Listing
January 2015

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

Amino Acids 2015 Jan 21;47(1):147-52. Epub 2014 Oct 21.

Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35131, Padua, Italy.

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http://link.springer.com/10.1007/s00726-014-1849-1
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http://dx.doi.org/10.1007/s00726-014-1849-1DOI Listing
January 2015

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

Nucleic Acids Res 2015 Jan 31;43(Database issue):D315-20. Epub 2014 Oct 31.

Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy

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http://dx.doi.org/10.1093/nar/gku982DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384034PMC
January 2015

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

Biochem Biophys Res Commun 2014 Aug 12;450(4):1606-11. Epub 2014 Jul 12.

Dept. of Biomedical Sciences, University of Padova, Padova, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2014.07.038DOI Listing
August 2014

PASTA 2.0: an improved server for protein aggregation prediction.

Nucleic Acids Res 2014 Jul 21;42(Web Server issue):W301-7. Epub 2014 May 21.

INFN, Padova Section, and Department of Physics and Astronomy 'G. Galilei', University of Padova, Padova I-35121, Italy.

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http://dx.doi.org/10.1093/nar/gku399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086119PMC
July 2014

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

Amino Acids 2014 Apr 23;46(4):853-62. Epub 2013 Dec 23.

Department of Biology, University of Padua, Viale G. Colombo 3, 35131, Padua, Italy,

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http://dx.doi.org/10.1007/s00726-013-1645-3DOI Listing
April 2014

RepeatsDB: a database of tandem repeat protein structures.

Nucleic Acids Res 2014 Jan 5;42(Database issue):D352-7. Epub 2013 Dec 5.

Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy, Department of Biological Chemistry, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina, Department of Information Engineering, University of Padua, 35121 Padova, Italy, Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan, Centre de Recherches de Biochimie Macromoléculaire, CNRS, 34293 Montpellier Cedex 5, France and Institut de Biologie Computationnelle, 34293 Montpellier Cedex 5, France.

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http://dx.doi.org/10.1093/nar/gkt1175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964956PMC
January 2014

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

BMC Bioinformatics 2013 22;14 Suppl 7:S3. Epub 2013 Apr 22.

Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.

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http://dx.doi.org/10.1186/1471-2105-14-S7-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633070PMC
December 2013

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

FEBS Open Bio 2013 24;3:310-20. Epub 2013 Jul 24.

Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956,C1113AAD Buenos Aires, Argentina.

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http://dx.doi.org/10.1016/j.fob.2013.07.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3741918PMC
August 2013

RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures.

Bioinformatics 2012 Dec 8;28(24):3257-64. Epub 2012 Sep 8.

Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/bts550DOI Listing
December 2012

MobiDB: a comprehensive database of intrinsic protein disorder annotations.

Bioinformatics 2012 Aug 1;28(15):2080-1. Epub 2012 Jun 1.

Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/bts327DOI Listing
August 2012

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

Bioinformatics 2012 Aug 17;28(16):2189-90. Epub 2012 Jun 17.

Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/bts343DOI Listing
August 2012

ESpritz: accurate and fast prediction of protein disorder.

Bioinformatics 2012 Feb 20;28(4):503-9. Epub 2011 Dec 20.

Department of Biology, University of Padua, Viale G. Colombo 3, I-35131 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btr682DOI Listing
February 2012

Identification and in silico analysis of novel von Hippel-Lindau (VHL) gene variants from a large population.

Ann Hum Genet 2011 Jul 4;75(4):483-96. Epub 2011 Apr 4.

Department of Pediatrics, University of Padua, Italy Department of Biology, University of Padua, Italy.

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http://dx.doi.org/10.1111/j.1469-1809.2011.00647.xDOI Listing
July 2011

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

Bioinformatics 2011 Jul 14;27(14):2003-5. Epub 2011 Apr 14.

Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btr191DOI Listing
July 2011

Immune roles of a rhamnose-binding lectin in the colonial ascidian Botryllus schlosseri.

Immunobiology 2011 Jun 4;216(6):725-36. Epub 2010 Nov 4.

Department of Biology, University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy.

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https://linkinghub.elsevier.com/retrieve/pii/S01712985100019
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http://dx.doi.org/10.1016/j.imbio.2010.10.011DOI Listing
June 2011

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

Bioinformatics 2010 Nov 21;26(22):2916-7. Epub 2010 Sep 21.

Department of Biology, University of Padova, viale G. Colombo 3, 35131 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btq537DOI Listing
November 2010