Publications by authors named "Anna Tramontano"

100Publications

Pregnant woman infected by Coronavirus Disease (COVID-19) and calcifications of the fetal bowel and gallbladder: a case report.

Minerva Ginecol 2020 Nov 30. Epub 2020 Nov 30.

Prenatal Medicine Unit, Obstetrics and Gynecology Unit, Department of Medical and Surgical Sciences for Mother, Child and Adult, University of Modena and Reggio Emilia, Modena, Italy -

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November 2020

Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling.

Sci Rep 2018 10 26;8(1):15895. Epub 2018 Oct 26.

Department of Biology and Biotechnology, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, 00185, Italy.

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October 2018

Evaluation of the template-based modeling in CASP12.

Proteins 2018 03 4;86 Suppl 1:321-334. Epub 2017 Dec 4.

Department of Biochemical Sciences, Sapienza - University of Rome, P. le A. Moro, 5, Rome, 00185.

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March 2018

The computational prediction of protein assemblies.

Authors:
Anna Tramontano

Curr Opin Struct Biol 2017 10 5;46:170-175. Epub 2017 Nov 5.

Physics Department, Sapienza University of Rome, Piazzale Aldo Moro, 5 I-00185 Roma, Italy; Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro, 5 I-00185 Roma, Italy.

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October 2017

Critical assessment of methods of protein structure prediction (CASP)-Round XII.

Proteins 2018 03 15;86 Suppl 1:7-15. Epub 2017 Dec 15.

Department of Physics and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University of Rome, P.le Aldo Moro, 5, Rome, 00185, Italy.

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March 2018

Assessment of model accuracy estimations in CASP12.

Proteins 2018 03 8;86 Suppl 1:345-360. Epub 2017 Sep 8.

Department of Physics, Sapienza University of Rome, Rome, Italy.

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March 2018

Dynamics behind affinity maturation of an anti-HCMV antibody family influencing antigen binding.

FEBS Lett 2017 09 30;591(18):2936-2950. Epub 2017 Aug 30.

Department of Physics, Sapienza - Università di Roma, Italy.

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September 2017

A computational approach for the functional classification of the epigenome.

Epigenetics Chromatin 2017 15;10:26. Epub 2017 May 15.

Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy.

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July 2017

PIGSPro: prediction of immunoGlobulin structures v2.

Nucleic Acids Res 2017 07;45(W1):W17-W23

Department of Physics, Sapienza University, Piazzale Aldo Moro 500-184 Rome, Italy.

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July 2017

Genome-wide identification of direct HBx genomic targets.

BMC Genomics 2017 02 17;18(1):184. Epub 2017 Feb 17.

Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome, 00161, Italy.

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February 2017

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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September 2016

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.

Proteins 2016 09 1;84 Suppl 1:4-14. Epub 2016 Jun 1.

Department of Physics and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy.

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September 2016

PepComposer: computational design of peptides binding to a given protein surface.

Nucleic Acids Res 2016 07 30;44(W1):W522-8. Epub 2016 Apr 30.

Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy Istituto Pasteur-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy.

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July 2016

A structural view of microRNA-target recognition.

Nucleic Acids Res 2016 05 28;44(9):e82. Epub 2016 Jan 28.

Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy Istituto Pasteur-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy

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May 2016

Prediction of the permeability of neutral drugs inferred from their solvation properties.

Bioinformatics 2016 04 10;32(8):1163-9. Epub 2015 Dec 10.

Department of Physics, Sapienza Università di Roma, Rome 00185, Italy Institute Pasteur - Fondazione Cenci Bolognetti, Rome, 00161, Italy Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Sapienza Università di Roma, Rome, 00185, Italy.

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April 2016

Exploiting homology information in nontemplate based prediction of protein structures.

J Chem Theory Comput 2015 Oct 30;11(10):5045-51. Epub 2015 Sep 30.

Department of Physics, Sapienza University of Rome , P.le A. Moro 4, 00185 Rome, Italy.

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October 2015

New encouraging developments in contact prediction: Assessment of the CASP11 results.

Proteins 2016 09 17;84 Suppl 1:131-44. Epub 2015 Nov 17.

Genome Center, University of California, Davis, California, 95616.

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September 2016

All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore.

J Phys Chem Lett 2015 Aug 16;6(15):2963-8. Epub 2015 Jul 16.

∥Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Via Regina Elena 291, 00161, Roma, Italia.

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August 2015

LoopIng: a template-based tool for predicting the structure of protein loops.

Bioinformatics 2015 Dec 6;31(23):3767-72. Epub 2015 Aug 6.

Department of Physics, Sapienza University, 00185 Rome, Italy and Istituto Pasteur-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy.

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December 2015

RNA editing differently affects protein-coding genes in D. melanogaster and H. sapiens.

Sci Rep 2015 Jul 14;5:11550. Epub 2015 Jul 14.

1] Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy [2] Instituto Pasteur-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, Rome 00185, Italy.

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July 2015

Multistep current signal in protein translocation through graphene nanopores.

J Phys Chem B 2015 May 28;119(18):5815-23. Epub 2015 Apr 28.

⊥Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Via Regina Elena 291, 00161 Roma, Italy.

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May 2015

3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments.

Bioinformatics 2015 Jun 22;31(11):1845-7. Epub 2015 Jan 22.

Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy.

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June 2015

Digestive peptidase evolution in holometabolous insects led to a divergent group of enzymes in Lepidoptera.

Insect Biochem Mol Biol 2015 Mar 17;58:1-11. Epub 2015 Jan 17.

Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900 Piracicaba, SP, Brazil. Electronic address:

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March 2015

Novel long noncoding RNAs (lncRNAs) in myogenesis: a miR-31 overlapping lncRNA transcript controls myoblast differentiation.

Mol Cell Biol 2015 Feb 15;35(4):728-36. Epub 2014 Dec 15.

Dept. of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy Institute Pasteur Fondazione Cenci-Bolognetti and IBPM, Sapienza University of Rome, Rome, Italy

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February 2015

Antibody modeling using the prediction of immunoglobulin structure (PIGS) web server [corrected].

Nat Protoc 2014 Dec 6;9(12):2771-83. Epub 2014 Nov 6.

1] Physics Department, Sapienza University of Rome, Piazzale Aldo Moro, Rome, Italy. [2] Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy.

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December 2014

Tabhu: tools for antibody humanization.

Bioinformatics 2015 Feb 9;31(3):434-5. Epub 2014 Oct 9.

Department of Physics, Sapienza University, Rome 00185, Italy, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Anker Engelunds Vej 1, 2800 Lyngby, Denmark and Istituto Pasteur-Fondazione Cenci Bolognetti, Rome 00185, Italy Department of Physics, Sapienza University, Rome 00185, Italy, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Anker Engelunds Vej 1, 2800 Lyngby, Denmark and Istituto Pasteur-Fondazione Cenci Bolognetti, Rome 00185, Italy.

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February 2015

Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach.

J Chem Theory Comput 2014 Sep;10(9):3589-97

CNR-Istituto dei Sistemi Complessi (ISC) , Via dei Taurini 19, I-00185, Rome, Italy.

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September 2014

Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies.

Bioinformatics 2014 Oct 13;30(19):2733-40. Epub 2014 Jun 13.

Department of Physics, Sapienza University, 00185 Rome, Italy, Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark and Istituto Pasteur-Fondazione Cenci Bolognetti, 00185 Rome, Italy Department of Physics, Sapienza University, 00185 Rome, Italy, Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark and Istituto Pasteur-Fondazione Cenci Bolognetti, 00185 Rome, Italy.

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October 2014

Critical assessment of methods of protein structure prediction (CASP)--round x.

Proteins 2014 Feb 17;82 Suppl 2:1-6. Epub 2013 Dec 17.

Institute for Bioscience and Biotechnology Research and Department of Cell Biology and Molecular Genetics, University of Maryland, Rockville, Maryland, 20850.

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February 2014

Assessment of protein disorder region predictions in CASP10.

Proteins 2014 Feb 22;82 Suppl 2:127-37. Epub 2013 Nov 22.

Genome Center University of California, Davis, Davis, California, 95616.

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February 2014

Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.

Bioinformatics 2013 Sep 26;29(18):2285-91. Epub 2013 Jun 26.

Department of Physics, Sapienza University and Istituto Pasteur - Fondazione Cenci Bolognetti, 00185 Rome, Italy.

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September 2013

Assessment of the assessment: evaluation of the model quality estimates in CASP10.

Proteins 2014 Feb 31;82 Suppl 2:112-26. Epub 2013 Aug 31.

Genome Center, University of California, Davis, 95616 California, USA.

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February 2014

Evaluation of residue-residue contact prediction in CASP10.

Proteins 2014 Feb 31;82 Suppl 2:138-53. Epub 2013 Aug 31.

Genome Center, University of California, Davis, California, 95616.

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February 2014

FIDEA: a server for the functional interpretation of differential expression analysis.

Nucleic Acids Res 2013 Jul 10;41(Web Server issue):W84-8. Epub 2013 Jun 10.

Department of Physics, Sapienza University, Rome, 00185, Italy.

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July 2013

TiPs: a database of therapeutic targets in pathogens and associated tools.

Bioinformatics 2013 Jul 21;29(14):1821-2. Epub 2013 May 21.

Department of Physics, Sapienza University, 00185 Rome, Italy.

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July 2013

Endocytosis of synaptic ADAM10 in neuronal plasticity and Alzheimer's disease.

J Clin Invest 2013 Jun 8;123(6):2523-38. Epub 2013 May 8.

Università degli Studi di Milano, Dipartimento di Scienze Farmacologiche e Biomolecolari and Centre of Excellence on Neurodegenerative Diseases, Milan, Italy.

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June 2013

The PARIGA server for real time filtering and analysis of reciprocal BLAST results.

PLoS One 2013 7;8(5):e62224. Epub 2013 May 7.

CRS4 Bioinformatics Laboratory, Science and Technology Park Polaris, Pula, Italy.

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December 2013

Massive screening of copy number population-scale variation in Bos taurus genome.

BMC Genomics 2013 Feb 26;14:124. Epub 2013 Feb 26.

Department for innovation in biological, agro-food and forest systems, University of Tuscia, via de Lellis, Viterbo 01100, Italy.

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February 2013

MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.

Bioinformatics 2013 Apr 8;29(7):953-4. Epub 2013 Feb 8.

Department of Physics, Sapienza University, 00185 Rome, Italy.

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April 2013

ProCoCoA: A quantitative approach for analyzing protein core composition.

Comput Biol Chem 2013 Apr 31;43:29-34. Epub 2012 Dec 31.

Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy.

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April 2013

A resource for benchmarking the usefulness of protein structure models.

BMC Bioinformatics 2012 Aug 2;13:188. Epub 2012 Aug 2.

Department of Physics, Sapienza University of Rome, P,le A, Moro, 5, 00185 Rome, Italy.

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August 2012

Detecting mutually exclusive interactions in protein-protein interaction maps.

PLoS One 2012 8;7(6):e38765. Epub 2012 Jun 8.

Department of Physics, Sapienza University of Rome, Rome, Italy.

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February 2015

Toward a better understanding of the interaction between TGF-β family members and their ALK receptors.

J Mol Model 2012 Aug 22;18(8):3617-25. Epub 2012 Feb 22.

Department of Chemical Sciences, Federico II University of Naples, Via Cinthia 45, 80126, Naples, Italy.

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August 2012

Improving your target-template alignment with MODalign.

Bioinformatics 2012 Apr 4;28(7):1038-9. Epub 2012 Feb 4.

Department of Physics, Sapienza University P.le A. Moro, 5, 00185 Rome, Italy.

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April 2012

Investigation of a potential mechanism for the inhibition of SmTGR by Auranofin and its implications for Plasmodium falciparum inhibition.

Biochem Biophys Res Commun 2012 Jan 8;417(1):576-81. Epub 2011 Dec 8.

Department of Physics, Sapienza University of Rome, Rome, Italy.

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January 2012

A database of immunoglobulins with integrated tools: DIGIT.

Nucleic Acids Res 2012 Jan 10;40(Database issue):D1230-4. Epub 2011 Nov 10.

Department of Physics, Sapienza University of Rome, P.le A Moro 5-00185, Italy.

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January 2012

Horizontal and vertical growth of S. cerevisiae metabolic network.

BMC Evol Biol 2011 Oct 14;11:301. Epub 2011 Oct 14.

Physics Department, Sapienza University of Rome, Roma, Italy.

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October 2011

Critical assessment of methods of protein structure prediction (CASP)--round IX.

Proteins 2011 14;79 Suppl 10:1-5. Epub 2011 Oct 14.

Institute for Bioscience and Biotechnology Research, and Department of Cell Biology and Molecular Genetics, University of Maryland, Rockville, MD 20850, USA.

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December 2011

Evaluation of model quality predictions in CASP9.

Proteins 2011 14;79 Suppl 10:91-106. Epub 2011 Oct 14.

Genome Center, University of California-Davis, 451 Health Sciences Drive, Davis, CA 95616, USA.

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December 2011

Identification of the Schistosoma mansoni molecular target for the antimalarial drug artemether.

J Chem Inf Model 2011 Nov 28;51(11):3005-16. Epub 2011 Oct 28.

Department of Physics, Sapienza University of Rome, Rome, Italy.

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November 2011

Evaluation of disorder predictions in CASP9.

Proteins 2011 16;79 Suppl 10:107-18. Epub 2011 Sep 16.

Genome Center, University of California-Davis, 451 Health Sciences Drive, Davis, CA 95616, USA

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December 2011

Evaluation of residue-residue contact predictions in CASP9.

Proteins 2011 17;79 Suppl 10:119-25. Epub 2011 Sep 17.

Genome Center, University of California-Davis, 451 Health Sciences Drive, Davis, CA 95616, USA

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December 2011

Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs.

PLoS One 2011 20;6(7):e22270. Epub 2011 Jul 20.

Department of Physics, Sapienza University of Rome, Rome, Italy.

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December 2011

Simulation of urea-induced protein unfolding: a lesson from bovine β-lactoglobulin.

J Mol Graph Model 2011 Sep 13;30:24-30. Epub 2011 Jun 13.

Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano, via Giuseppe Balzaretti 9, 20133 Milano, Italy.

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September 2011

The association of heavy and light chain variable domains in antibodies: implications for antigen specificity.

FEBS J 2011 Aug 28;278(16):2858-66. Epub 2011 Jun 28.

Department of Physics, Sapienza University of Rome, Italy.

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August 2011

MAISTAS: a tool for automatic structural evaluation of alternative splicing products.

Bioinformatics 2011 Jun 15;27(12):1625-9. Epub 2011 Apr 15.

CRS4-Bioinformatics Laboratory, c/o Sardegna Ricerche Scientific Park, Pula, 09010 Cagliari, Italy.

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June 2011

Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract.

BMC Evol Biol 2011 Mar 19;11:72. Epub 2011 Mar 19.

Istituto-Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, 'Sapienza' Università di Roma, Italy.

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March 2011

Novel cinnamyl hydroxyamides and 2-aminoanilides as histone deacetylase inhibitors: apoptotic induction and cytodifferentiation activity.

ChemMedChem 2011 Apr 4;6(4):698-712. Epub 2011 Mar 4.

Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy.

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April 2011

Structural repertoire of immunoglobulin λ light chains.

Proteins 2011 May 1;79(5):1513-24. Epub 2011 Mar 1.

Department of Biochemical Sciences, Sapienza University of Rome, P.le A. Moro, 5-00185 Rome (I), Italy.

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May 2011

Coding potential of the products of alternative splicing in human.

Genome Biol 2011 20;12(1):R9. Epub 2011 Jan 20.

Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, P.le A. Moro, 5 - 00185 Rome, Italy.

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February 2012

On the mechanism of chloroquine resistance in Plasmodium falciparum.

PLoS One 2010 Nov 19;5(11):e14064. Epub 2010 Nov 19.

Department of Biochemical Sciences, Sapienza University, Rome, Italy.

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November 2010

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.

Nucleic Acids Res 2011 Jan 21;39(Database issue):D268-71. Epub 2010 Oct 21.

Institute for Research in Biomedicine, Joint IRB-BSC program in Computational Biology, 08028 Barcelona, Spain.

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January 2011

PICMI: mapping point mutations on genomes.

Bioinformatics 2010 Nov 12;26(22):2904-5. Epub 2010 Oct 12.

Department of Biochemical Sciences, Sapienza University of Rome, P.le A. Moro, 5-00185 Rome, Italy.

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November 2010

An automatic method for identifying surface proteins in bacteria: SLEP.

BMC Bioinformatics 2010 Jan 20;11:39. Epub 2010 Jan 20.

Department of Biochemical Sciences A, Rossi Fanelli, Sapienza University, 00185 Rome, Italy.

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January 2010

In memoriam. Angel Ramírez Ortiz (1966-2008).

Proteins 2010 Jan;78(1):iii-viii

Bioinformatics Unit, Centro de Biología Molecular Severo Ochoa, Madrid, Spain.

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January 2010

Site-directed enzymatic PEGylation of the human granulocyte colony-stimulating factor.

FEBS J 2009 Nov 16;276(22):6741-50. Epub 2009 Oct 16.

Bio-Ker Srl, c/o Sardegna Ricerche Scientific Park, Pula, Cagliari, Italy.

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November 2009

Critical assessment of methods of protein structure prediction - Round VIII.

Proteins 2009 ;77 Suppl 9:1-4

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

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January 2010

Evaluation of template-based models in CASP8 with standard measures.

Proteins 2009 ;77 Suppl 9:18-28

Department of Biochemical Sciences, Sapienza-University of Rome, P. le A. Moro, 5, 00185 Rome, Italy.

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January 2010

Evaluation of CASP8 model quality predictions.

Proteins 2009 ;77 Suppl 9:157-66

Department of Biochemical Sciences, Sapienza - University of Rome, Rome 00185, Italy.

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January 2010

No protein is an island.

Authors:
Anna Tramontano

Curr Opin Struct Biol 2009 Jun 30;19(3):310-1. Epub 2009 May 30.

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June 2009

Protein function annotation by homology-based inference.

Genome Biol 2009 Feb 2;10(2):207. Epub 2009 Feb 2.

Department of Biological Chemistry, The Hebrew University of Jerusalem, Sudarsky Center, Jerusalem 91904, Israel.

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February 2009

Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase Itch and the E2 UbcH7.

Biochem Pharmacol 2008 Dec 31;76(11):1620-7. Epub 2008 Aug 31.

Department of Biochemical Sciences "Rossi-Fanelli", University of Rome "La Sapienza", P.le Aldo Moro 5, Rome, Italy.

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December 2008

PIGS: automatic prediction of antibody structures.

Bioinformatics 2008 Sep 19;24(17):1953-4. Epub 2008 Jul 19.

Department of Biochemical Sciences and Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza University, P.le A. Moro 5, 00185 Rome, Italy.

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September 2008

Comparative modelling techniques: where are we?

Authors:
Anna Tramontano

Comp Funct Genomics 2003 ;4(4):402-5

Department of Biochemical Sciences A. Rossi Fanelli, University of Rome La Sapienza, Rome 00185, Italy.

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June 2010

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.

BMC Bioinformatics 2008 Mar 26;9 Suppl 2:S2. Epub 2008 Mar 26.

Centre for Molecular Bioinformatics, Department of Biology, University of Rome "Tor Vergata", Rome, Italy.

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March 2008

The MoVIN server for the analysis of protein interaction networks.

BMC Bioinformatics 2008 Mar 26;9 Suppl 2:S11. Epub 2008 Mar 26.

Department of Biochemical Sciences, "Sapienza" University, Rome, Italy.

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March 2008

The assessment of methods for protein structure prediction.

Methods Mol Biol 2008 ;413:43-57

Department of Biochemical Sciences, University of Rome, "La Sapienza" Rome, Italy.

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June 2008

The evaluation of protein structure prediction results.

Mol Biotechnol 2008 May 11;39(1):1-8. Epub 2007 Dec 11.

Department of Biochemical Sciences Rossi Fanelli, University of Rome La Sapienza, P. le A. Moro, 5, 00185, Rome, Italy.

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May 2008

Yeast as a model of human mitochondrial tRNA base substitutions: investigation of the molecular basis of respiratory defects.

RNA 2008 Feb 7;14(2):275-83. Epub 2007 Dec 7.

Department of Cell and Developmental Biology, Pasteur Institute-Fondazione Cenci Bolognetti, University Sapienza, 00185 Rome, Italy.

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February 2008

Critical assessment of methods of protein structure prediction-Round VII.

Proteins 2007 ;69 Suppl 8:3-9

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

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January 2008

Assessment of predictions in the model quality assessment category.

Proteins 2007 ;69 Suppl 8:175-83

Department of Biochemical Sciences, University of Rome La Sapienza, P. le A. Moro, 00185 Rome, Italy.

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January 2008