A. Tramontano

发表

Relationship between multiple sequence alignments and quality of protein comparative models

D. Cozzetto, A. Tramontano, 2004, Proteins.

Detecting Mutually Exclusive Interactions in Protein-Protein Interaction Maps

A. Tramontano, Carmen Sánchez Claros, 2012, PloS one.

Critical assessment of methods of protein structure prediction—Round VIII

B. Rost, A. Tramontano, K. Fidelis, 2009, Proteins.

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

A. Tramontano, K. Fidelis, J. Moult, 2011, Proteins.

Protein function annotation by homology-based inference

C. Orengo, D. Frishman, A. Tramontano, 2009, Genome Biology.

Evaluation of residue–residue contact predictions in CASP9

A. Tramontano, K. Fidelis, Andriy Kryshtafovych, 2011, Proteins.

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

D. Cacchiarelli, A. Tramontano, I. Bozzoni, 2011, Cell.

Genome sequences and great expectations

C. Sander, A. Valencia, C. Ouzounis, 2000, Genome Biology.

Conformations of immunoglobulin hypervariable regions

A. Lesk, C. Chothia, M. Levitt, 1989, Nature.

Structural repertoire of immunoglobulin λ light chains

A. Tramontano, D. Cirillo, P. Marcatili, 2011, Proteins.

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

A. Tramontano, K. Fidelis, J. Moult, 2016, Proteins.

Critical assessment of methods of protein structure prediction (CASP)—Round 6

B. Rost, T. Hubbard, A. Tramontano, 2005 .

Protein Structural Motifs : Identification , Annotation and Use in Function Prediction Allegra Via

A. Tramontano, A. Via, 2011 .

Evaluation of residue–residue contact prediction in CASP10

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2014, Proteins.

Protein structure prediction and design.

A. Tramontano, R. Leplae, V. Morea, 1998, Biotechnology annual review.

PUZZLE: a new method for automated protein docking based on surface shape complementarity.

A Tramontano, A. Tramontano, M. Helmer-Citterich, 1994, Journal of molecular biology.

Mapping the hydropathy of amino acids based on their local solvation structure.

A Tramontano, G. Ciccotti, A. Tramontano, 2014, The journal of physical chemistry. B.

Coding potential of the products of alternative splicing in human

A. Tramontano, F. Ferrè, D. Raimondo, 2011, Genome Biology.

Small molecule inhibitors of histone arginine methyltransferases: homology modeling, molecular docking, binding mode analysis, and biological evaluations.

A. Tramontano, A. Mai, P. Trojer, 2007, Journal of medicinal chemistry.

The biological applications of protein models

A. Tramontano, 2008 .

Structural determinants of the conformations of medium‐sized loops in proteins

A. Lesk, C. Chothia, A. Tramontano, 1989, Proteins.

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

A. Tramontano, K. Fidelis, Andriy Kryshtafovych, 2016, Proteins.

Common features of the conformations of antigen‐binding loops in immunoglobulins and application to modeling loop conformations

A. Lesk, A. Tramontano, Arthur M. Lesk, 1992, Proteins.

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

A. Tramontano, K. Fidelis, J. Moult, 2018, Proteins.

Classification of proteins based on the properties of the ligand‐binding site: The case of adenine‐binding proteins

A. Tramontano, V. Cappello, U. Koch, 2002, Proteins.

Advances and pitfalls in protein structure prediction.

D. Cozzetto, A. Tramontano, 2008, Current protein & peptide science.

Conformations of the third hypervariable region in the VH domain of immunoglobulins.

A Tramontano, V Morea, A M Lesk, 1998, Journal of molecular biology.

Stereotyped patterns of B-cell receptor in splenic marginal zone lymphoma

Anna Tramontano, Francesco Bertoni, Paolo Marcatili, 2010, Haematologica.

Igs Expressed by Chronic Lymphocytic Leukemia B Cells Show Limited Binding-Site Structure Variability

Anna Tramontano, Paolo Marcatili, Silvia Bruno, 2013, The Journal of Immunology.

Exploiting evolutionary relationships for predicting protein structures

Anna Tramontano, Veronica Morea, A. Tramontano, 2003, Biotechnology and bioengineering.

Integral and differential form of the protein folding problem

A. Tramontano, 2004 .

Structural conservation in single-domain proteins: implications for homology modeling.

A Tramontano, A. Tramontano, A. Lahm, 2001, Journal of structural biology.

Evaluation of disorder predictions in CASP9

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2011, Proteins.

Evaluation of model quality predictions in CASP9

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2011, Proteins.

Probing the tertiary structure of proteins by limited proteolysis and mass spectrometry: The case of minibody

Anna Tramontano, Gennaro Marino, Francesca Zappacosta, 1996, Protein science : a publication of the Protein Society.

Automatic procedure for using models of proteins in molecular replacement

Anna Tramontano, Domenico Raimondo, Alejandro Giorgetti, 2006, Proteins.

In memoriam

A. Tramontano, P. Chacón, U. Bastolla, 2009, Proteins.

Structure prediction of globular proteins

David T. Jones, A. Tramontano, R. Casadio, 2008 .

The role of molecular modelling in biomedical research

Anna Tramontano, A. Tramontano, 2006, FEBS letters.

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

A. Tramontano, D. Raimondo, Francesco Baldini, 2011, BMC Evolutionary Biology.

The computational prediction of protein assemblies.

A. Tramontano, 2017, Current opinion in structural biology.

Multistep current signal in protein translocation through graphene nanopores.

A. Tramontano, F. Cecconi, D. Raimondo, 2015, The journal of physical chemistry. B.

Novel Cinnamyl Hydroxyamides and 2‐Aminoanilides as Histone Deacetylase Inhibitors: Apoptotic Induction and Cytodifferentiation Activity

A. Tramontano, L. Altucci, A. Mai, 2011, ChemMedChem.

The Architecture of Loops in Proteins

A. Tramontano, 1996 .

Title : Assessment of model accuracy estimations in CASP 12 Short title : Model accuracy assessment

A. Tramontano, K. Fidelis, Andriy Kryshtafovych, 2017 .

Horizontal and vertical growth of S. cerevisiae metabolic network

A. Tramontano, L. Grassi, 2011, BMC Evolutionary Biology.

Antibody structural modeling with prediction of immunoglobulin structure (PIGS)

Anna Tramontano, Paolo Marcatili, Pier Paolo Olimpieri, 2014 .

Dissecting the Structural Determinants of the Interaction between the Human Cytomegalovirus UL18 Protein and the CD85j Immune Receptor1

M. Nardini, A. Tramontano, S. Bruno, 2008, The Journal of Immunology.

On the Mechanism of Chloroquine Resistance in Plasmodium falciparum

A. Tramontano, M. Chinappi, P. Marcatili, 2010, PloS one.

Variability within the Candida rugosa lipases family.

L. Alberghina, A. Tramontano, S. Longhi, 1994, Protein engineering.

Inhibition of endothelial cell migration and angiogenesis by a vascular endothelial growth factor receptor-1 derived peptide.

A. Tramontano, L. Tentori, P. Lacal, 2008, European journal of cancer.

Protein structure prediction: playing the fold.

T. Hubbard, J. Park, A. Tramontano, 1996, Trends in biochemical sciences.

Exploiting Publicly Available Biological and Biochemical Information for the Discovery of Novel Short Linear Motifs

A. Tramontano, A. Via, A. Sayadi, 2011, PloS one.

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

A. Tramontano, D. Raimondo, Valentina Romano, 2012, Journal of Molecular Modeling.

Managing Your Biological Data with Python

Kristian Rother, Allegra Via, Anna Tramontano, 2014 .

Coordinated and reversible reduction of enzymes involved in terminal oxidative metabolism in skeletal muscle mitochondria from a riboflavin‐responsive, multiple acyl‐CoA dehydrogenase deficiency patient

A. Tramontano, C. Angelini, E. Pegoraro, 2006, Electrophoresis.

Alternative Splicing in the ENCODE Protein complement

Gabrielle A. Reeves, G. A. Reeves, Peter F. Hallin, 2008 .

High level expression and rational mutagenesis of a designed protein, the minibody. From an insoluble to a soluble molecule.

A. Tramontano, E. Bianchi, M. Sollazzo, 1994, Journal of molecular biology.

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

A. Tramontano, Francesco Di Palma, 2017, FEBS letters.

Site‐directed enzymatic PEGylation of the human granulocyte colony‐stimulating factor

A. Tramontano, D. Raimondo, A. Giorgetti, 2009, The FEBS journal.

The implications of alternative splicing in the ENCODE protein complement

Hagen Blankenburg, Fidel Ramírez, Thomas Lengauer, 2007, Proceedings of the National Academy of Sciences.

Lipoprotein(a) Where Do We Stand? From the Physiopathology to Innovative Terapy

A. Tramontano, F. Giallauria, M. D. Di Minno, 2021, Biomedicines.

Rational design and functional expression of a constitutively active single-chain NS4A-NS3 proteinase.

A. Tramontano, R. De Francesco, A. Pasquo, 1998, Folding & design.

Mutations of Gly to Ala in human glutathione transferase P1-1 affect helix 2 (G-site) and induce positive cooperativity in the binding of glutathione.

A. Tramontano, M. Parker, A. Caccuri, 1998, Journal of molecular biology.

Rapid Profiling of the Antigen Regions Recognized by Serum Antibodies Using Massively Parallel Sequencing of Antigen-Specific Libraries

A. Tramontano, F. Felici, G. Teti, 2014, PloS one.

Surface topology of Minibody by selective chemical modifications and mass spectrometry

A. Tramontano, A. Scaloni, G. Marino, 1997, Protein science : a publication of the Protein Society.

Identification and functional characterization of the bile acid transport proteins in non‐mammalian ileum and mammalian liver

A. Tramontano, D. Raimondo, Serena Zanzoni, 2007, Proteins.

A computational approach for the functional classification of the epigenome

A. Tramontano, Francesco Gandolfi, 2017, Epigenetics & Chromatin.

Structure Variability Binding-Site Leukemia B Cells Show Limited Igs Expressed by Chronic Lymphocytic

A. Tramontano, Xiao-Jie Yan, N. Chiorazzi, 2013 .

, between Hypervariable Regions 1 and 2 Is Modulated by a Complex Interplay Glycoprotein to CD 81 Is Strain Specific and Binding of the Hepatitis C Virus E 2

A. Tramontano, A. Meola, R. Cortese, 2002 .

Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs.

A. Tramontano, L. Cavallo, R. Oliva, 2007, RNA.

Genome-wide identification of direct HBx genomic targets

A. Tramontano, F. Zoulim, M. Levrero, 2017, BMC Genomics.

Saturation mutagenesis of the human interleukin 6 receptor-binding site: implications for its three-dimensional structure.

A. Tramontano, G. Ciliberto, R. Savino, 1993, Proceedings of the National Academy of Sciences of the United States of America.

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

A. Tramontano, L. Grassi, G. Leoni, 2015, Scientific Reports.

A proangiogenic peptide derived from vascular endothelial growth factor receptor-1 acts through alpha5beta1 integrin.

A. Tramontano, P. Lacal, L. Morbidelli, 2008, Blood.

A proangiogenic peptide derived from vascular endothelial growth factor receptor-1 acts through α5β1 integrin

A. Tramontano, P. Lacal, L. Morbidelli, 2008 .

No protein is an island.

A. Tramontano, 2009, Current opinion in structural biology.

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

M. Bolotin-Fukuhara, L. Frontali, A. Tramontano, 2007, RNA.

IN MEMORIAM

A. Tramontano, P. Chacón, U. Bastolla, 1979, Science.

OP-CBIO150449 1..6

Mario Abdel Messih, A. Tramontano, R. Lepore, 2015 .

Aminoacylation and conformational properties of yeast mitochondrial tRNA mutants with respiratory deficiency.

L. Frontali, A. Tramontano, R. Oliva, 2005, RNA.

Induction of Cross-reactive Humoral Immune Response by Immunization with Mimotopes of the Hypervariable Region 1 of the Hepatitis C Virus

A. Tramontano, A. Folgori, R. Tafi, 2001, International reviews of immunology.

Affinity purification of a difficult-sequence protein. Implications for the inclusion of capping in synthetic protocols.

A. Tramontano, E. Bianchi, M. Sollazzo, 2009, International journal of peptide and protein research.

Book Reviews Protein Structure Prediction: Concepts and Applications

A. Tramontano, 2007 .

Exploring the Cytochrome c Folding Mechanism

M. Brunori, A. Tramontano, S. Gianni, 2003, Journal of Biological Chemistry.

SOLUTION STRUCTURES OF LARGE GROUP 5A AND 6A POLYOXOANIONS BY (17)O NUCLEAR MAGNETIC RESONANCE

A. Tramontano, J. Jesson, A. English, 1975 .

Superposition-free comparison and clustering of antibody binding sites: implications for the prediction of the nature of their antigen

Anna Tramontano, Pier Paolo Olimpieri, Rosalba Lepore, 2017, Scientific Reports.

A structure-guided approach to an orthogonal estrogen-receptor-based gene switch activated by ligands suitable for in vivo studies.

A. Tramontano, R. Cortese, G. Ciliberto, 2006, Journal of medicinal chemistry.

A database of immunoglobulins with integrated tools: DIGIT

Anna Tramontano, Anna Chailyan, Paolo Marcatili, 2011, Nucleic Acids Res..

Chemical synthesis of a designed β-protein through the flow-polyamide method

A. Tramontano, A. Pessi, E. Bianchi, 2009 .

Design of a small protein as a potential source of selectable peptide sequences of known structure

A. Tramontano, A. Pessi, E. Bianchi, 1995 .

Novel Long Noncoding RNAs (lncRNAs) in Myogenesis: a miR-31 Overlapping lncRNA Transcript Controls Myoblast Differentiation

A. Tramontano, I. Bozzoni, Tiziana Santini, 2014, Molecular and Cellular Biology.

Towards a solution for hepatitis C virus hypervariability: mimotopes of the hypervariable region 1 can induce antibodies cross‐reacting with a large number of viral variants

Anna Tramontano, Silvia Zucchelli, Armin Lahm, 1998, The EMBO journal.

The PMDB Protein Model Database

Anna Tramontano, Tiziana Castrignanò, Domenico Cozzetto, 2005, Nucleic Acids Res..

Anna Tramontano, Fabio Ghiotto, M. Nardini, 2004, The Journal of clinical investigation.

A model for recognition of polychlorinated dibenzo-p-dioxins by the aryl hydrocarbon receptor.

A Tramontano, A. Tramontano, D. Pitea, 2002, European journal of biochemistry.

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

A. Tramontano, A. Via, M. Silva-Filho, 2015, Insect biochemistry and molecular biology.

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

D. Cacchiarelli, A. Tramontano, I. Bozzoni, 2011, Cell.

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

Paolo Marcatili, Anna Tramontano, Pier Paolo Olimpieri, 2013, Bioinform..

The Snail repressor recruits EZH2 to specific genomic sites through the enrollment of the lncRNA HOTAIR in epithelial-to-mesenchymal transition

A. Tramontano, F. Gonzalez, L. Grassi, 2016, Oncogene.

A designed metal-binding protein with a novel fold

Anna Tramontano, A. Tramontano, A. Crameri, 1993, Nature.

An analysis of the Sargasso Sea resource and the consequences for database composition

Anna Tramontano, Alfonso Valencia, Michael L. Tress, 2006, BMC Bioinformatics.

A structural view of microRNA–target recognition

Anna Tramontano, Guido Leoni, A. Tramontano, 2016, Nucleic acids research.

A computational approach for the functional classification of the epigenome

A. Tramontano, Francesco Gandolfi, 2017, Epigenetics & Chromatin.

Thermodynamic characteristics of a biological organism: Information value of a gene and of a protein as a measure of the efficiency and as an index of selective pressure

A. Tramontano, V. Cuomo, M. Macchiato, 1983 .

The nonstructural proteins of the hepatitis C virus: structure and functions.

A. Tramontano, R. De Francesco, L. Tomei, 1997, Biological chemistry.

SAP97-mediated ADAM10 trafficking from Golgi outposts depends on PKC phosphorylation

A. Tramontano, B. Borroni, E. Marcello, 2014, Cell Death and Disease.

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

Anna Tramontano, Mariagiovanna Mazzapioda, Loredana Le Pera, 2015, Bioinform..

Bacteriophage lambda display of complex cDNA libraries: a new approach to functional genomics.

A. Tramontano, A. Nicosia, A. Luzzago, 2000, Journal of molecular biology.

Interactive program for visualization and modelling of proteins, nucleic acids and small molecules

R J Fletterick, A Tramontano, H E Dayringer, 1986 .

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

Anna Tramontano, Paolo Marcatili, Anna Chailyan, 2011, The FEBS journal.

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

Massimiliano Orsini, Paolo Marcatili, Matteo Floris, 2011, Bioinform..

Homology modeling with low sequence identity.

A Tramontano, A. Tramontano, 1998, Methods.

Analysis of a cDNA sequence encoding the immunoglobulin heavy chain of the Antarctic teleost Trematomus bernacchii.

A. Tramontano, V. Morea, M. Coscia, 2000, Fish & shellfish immunology.

Identification of the Schistosoma mansoni Molecular Target for the Antimalarial Drug Artemether

Anna Tramontano, Allegra Via, Domenico Raimondo, 2011, J. Chem. Inf. Model..

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

A. Tramontano, G. Chillemi, P. Ajmone-Marsan, 2013, BMC Genomics.

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

Anna Tramontano, Allegra Via, Manuela Helmer-Citterich, 2010, Nucleic Acids Res..

Identifying a putative common binding site shared by substance P receptor and an anti-substance P monoclonal antibody.

T. Werge, A. Tramontano, A. Cattaneo, 1995, Protein engineering.

Pregnant woman infected by Coronavirus disease (COVID-19) and calcifications of the fetal bowel and gallbladder

A. Tramontano, F. Facchinetti, L. Lugli, 2021 .

Assessment of the assessment: Evaluation of the model quality estimates in CASP10

Anna Tramontano, Alessandro Barbato, Torsten Schwede, 2014, Proteins.

Mutation Pattern of Paired Immunoglobulin Heavy and Light Variable Domains in Chronic Lymphocytic Leukemia B Cells

Anna Tramontano, Paolo Marcatili, Silvia Bruno, 2011, Molecular medicine.

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

Tapio Salakoski, Paolo Fontana, Silvio C. E. Tosatto, 2016, Genome Biology.

Analysis of Hepatitis C Virus Hypervariable Region 1 Sequence from Cryoglobulinemic Patients and Associated Controls

A. Tramontano, M. Mondelli, G. Bianchettin, 2007, Journal of Virology.

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

Anna Tramontano, Rosalba Lepore, Alfredo Iacoangeli, 2016, Nucleic Acids Res..

A resource for benchmarking the usefulness of protein structure models

A. Tramontano, D. Carbajo, 2012, BMC Bioinformatics.

The MoVIN server for the analysis of protein interaction networks

Paolo Marcatili, Anna Tramontano, Giovanni Bussotti, 2008, BMC Bioinformatics.

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

Anna Tramontano, Domenico Raimondo, Edoardo Milanetti, 2015, Bioinform..

Binding of the Hepatitis C Virus E2 Glycoprotein to CD81 Is Strain Specific and Is Modulated by a Complex Interplay between Hypervariable Regions 1 and 2

A. Tramontano, A. Meola, R. Cortese, 2003, Journal of Virology.

Members of the zinc finger protein gene family sharing a conserved N-terminal module.

A. Tramontano, G. Grimaldi, A. Franzè, 1991, Nucleic acids research.

The PARIGA Server for Real Time Filtering and Analysis of Reciprocal BLAST Results

Anna Tramontano, Massimiliano Orsini, Gianmauro Cuccuru, 2013, PloS one.

Cancer-Selective Targeting of the NF-κB Survival Pathway with GADD45β/MKK7 Inhibitors

A. Chambery, A. Tramontano, G. Morgan, 2014, Cancer cell.

Cancer-Selective Targeting of the NF-κB Survival Pathway with GADD45β/MKK7 Inhibitors

Anna Tramontano, Domenico Raimondo, Menotti Ruvo, 2014, Cancer cell.

Evaluation of annotation strategies using an entire genome sequence

Miguel A. Andrade-Navarro, Alfonso Valencia, Anton J. Enright, 2003, Bioinform..

Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches

Anna Tramontano, Marialuisa Pellegrini-Calace, A. Tramontano, 2006, Bioinform..

Sequence analysis Identiﬁcation of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches

A. Tramontano, M. Pellegrini-Calace, 2006 .

Mapping epitopes on protein surfaces.

A Tramontano, A. Tramontano, R. Cortese, 1995, Biopolymers.

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

A. Tramontano, G. Melino, D. Raimondo, 2008, Biochemical pharmacology.

Identification of biologically active peptides using random libraries displayed on phage.

A Tramontano, M Sollazzo, A. Tramontano, 1995, Current opinion in biotechnology.

The making of the minibody: An engineered β‐protein for the display of conformationally constrained peptides

A. Tramontano, E. Bianchi, S. Venturini, 1994, Journal of molecular recognition : JMR.

Modelling antibody-antigen interactions: ferritin as a case study.

E Rovida, A Tramontano, A. Tramontano, 1995, Molecular immunology.

Engineering stable cytoplasmic intrabodies with designed specificity.

Anna Tramontano, Veronica Morea, Eugenio Benvenuto, 2003, Journal of molecular biology.

Antibody modeling: implications for engineering and design.

A Tramontano, V Morea, A M Lesk, 2000, Methods.

Antibody structure, prediction and redesign.

A Tramontano, V Morea, A M Lesk, 1997, Biophysical chemistry.

Framework residue 71 is a major determinant of the position and conformation of the second hypervariable region in the VH domains of immunoglobulins.

A Tramontano, A M Lesk, C Chothia, 1990, Journal of molecular biology.

PIGS: automatic prediction of antibody structures

Paolo Marcatili, Anna Tramontano, Alessandra Rosi, 2008, Bioinform..

Critical assessment of methods of protein structure prediction—Round VII

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2007, Proteins.

A method to evaluate the relative weights of structural and functional constraints on a genome

A. Tramontano, M. Macchiato, C. Cosmi, 1991 .

An automatic method for identifying surface proteins in bacteria: SLEP

Anna Tramontano, Massimiliano Orsini, Danilo Carrabino, 2010, BMC Bioinformatics.

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

Anna Tramontano, Rosalba Lepore, Mario Abdel Messih, 2015, Bioinform..

The prediction of protein function at CASP6

Anna Tramontano, Simonetta Soro, A. Tramontano, 2005, Proteins.

The betaI/betaIII-tubulin isoforms and their complexes with antimitotic agents. Docking and molecular dynamics studies.

A. Tramontano, M. Botta, S. Soro, 2006, The FEBS journal.

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

M. Giustetto, A. Tramontano, B. Borroni, 2013, The Journal of clinical investigation.

Update on protein structure prediction: results of the 1995 IRBM workshop.

A Tramontano, T Hubbard, T. Hubbard, 1996, Folding & design.

The Relationship Between Protein Sequence, Structure and Function

Anna Tramontano, Domenico Cozzetto, D. Cozzetto, 2005 .

ProCoCoA: A quantitative approach for analyzing protein core composition

Anna Tramontano, Diego Garlaschelli, Andrea Bernini, 2013, Comput. Biol. Chem..

Cloning and analysis of Candida cylindracea lipase sequences.

L. Alberghina, A. Tramontano, S. Longhi, 1993, Gene.

Evaluating the usefulness of protein structure models for molecular replacement

Anna Tramontano, Domenico Raimondo, Alejandro Giorgetti, 2005, ECCB/JBI.

The ten most wanted solutions in protein bioinformatics

Anna Tramontano, A. Tramontano, 2005 .

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

Anna Tramontano, Torsten Schwede, Krzysztof Fidelis, 2014, Proteins.

PIGSPro: prediction of immunoGlobulin structures v2

Anna Tramontano, Pier Paolo Olimpieri, Rosalba Lepore, 2017, Nucleic Acids Res..

Antibody modeling using the Prediction of ImmunoGlobulin Structure (PIGS) web server

Anna Tramontano, Pier Paolo Olimpieri, Anna Chailyan, 2014, Nature Protocols.

A model of the complex between the PfEMP1 malaria protein and the human ICAM‐1 receptor

Anna Tramontano, A. Tramontano, C. Bertonati, 2007, Proteins.

Substrate Specificity of the Hepatitis C Virus Serine Protease NS3*

A Tramontano, A. Tramontano, A. Urbani, 1997, The Journal of Biological Chemistry.

Assessment of homology‐based predictions in CASP5

Anna Tramontano, Veronica Morea, A. Tramontano, 2003, Proteins.

Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition.

A Tramontano, A. Tramontano, R. De Francesco, 1994, Proceedings of the National Academy of Sciences of the United States of America.

VARIANT: a store and retrieval system for human haemoglobin variants.

A Tramontano, M F Macchiato, A. Tramontano, 1990, Computer methods and programs in biomedicine.

MD and Docking Studies Reveal That the Functional Switch of CYFIP1 is Mediated by a Butterfly-like Motion.

A. Tramontano, C. Bagni, G. Chillemi, 2015, Journal of chemical theory and computation.

Evolution of Bacterial and Archaeal Multicomponent Monooxygenases

A. Tramontano, A. Lahm, E. Notomista, 2003, Journal of Molecular Evolution.

Analysis and assessment of comparative modeling predictions in CASP4

R Leplae, A Tramontano, V Morea, 2001, Proteins.

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

Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich, 2008, BMC Bioinformatics.

Revisiting the prediction of protein function at CASP6

Anna Tramontano, Marialuisa Pellegrini-Calace, Simonetta Soro, 2006, The FEBS journal.

Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11

Anna Tramontano, Alessandro Barbato, Torsten Schwede, 2016, Proteins.

Mimicking of discontinuous epitopes by phage-displayed peptides, I. Epitope mapping of human H ferritin using a phage library of constrained peptides.

A. Tramontano, F. Felici, R. Cortese, 1993, Gene.

Assessment of predictions in the model quality assessment category

Anna Tramontano, Domenico Cozzetto, Andriy Kryshtafovych, 2007, Proteins.

Protein structure prediction

Anna Tramontano, A. Tramontano, 2013 .

Evaluation of template‐based models in CASP8 with standard measures

Burkhard Rost, Anna Tramontano, Domenico Cozzetto, 2009, Proteins.

Characterization of the differences in the cyclopiazonic acid binding mode to mammalian and P. Falciparum Ca2+ pumps: A computational study

A. Tramontano, A. Via, A. Coletta, 2015, Proteins.

Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions

Anna Tramontano, Luigi Cavallo, Romina Oliva, 2006, Nucleic acids research.

A model for the hepatitis C virus envelope glycoprotein E2

Anna Tramontano, Armin Lahm, A. Tramontano, 2000, Proteins.

Mimotopes of the hyper variable region 1 of the hepatitis C virus induce cross-reactive antibodies directed against discontinuous epitopes.

A. Tramontano, A. Folgori, R. Tafi, 2001, Molecular immunology.

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

A. Tramontano, R. Lepore, M. Possenti, 2018, Scientific Reports.

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

Anna Tramontano, Mariagiovanna Mazzapioda, Daniel D'Andrea, 2013, Nucleic Acids Res..

In Vivo Selection of Protease Cleavage Sites by Using Chimeric Sindbis Virus Libraries

A. Tramontano, L. Pacini, L. Bartholomew, 2000, Journal of Virology.

A zinc binding site in viral serine proteinases.

A. Tramontano, A. Urbani, R. De Francesco, 1996, Biochemistry.

Selection of Functional Variants of the NS3-NS4A Protease of Hepatitis C Virus by Using Chimeric Sindbis Viruses

A. Tramontano, M. Scaturro, L. Pacini, 1999, Journal of Virology.

Evaluation of the template‐based modeling in CASP12

Anna Tramontano, Torsten Schwede, Krzysztof Fidelis, 2018, Proteins.

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

A. Tramontano, A. Pedretti, L. Ragona, 2011, Journal of molecular graphics & modelling.

Network cleansing: Reliable interaction networks

Anna Tramontano, Paolo Marcatili, A. Tramontano, 2009 .

Assessment of protein disorder region predictions in CASP10

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2014, Proteins.

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

A. Tramontano, M. Chinappi, D. Di Marino, 2015, The journal of physical chemistry letters.

The βI/βIII‐tubulin isoforms and their complexes with antimitotic agents

A. Tramontano, M. Botta, S. Soro, 2006 .

Structural definition by antibody engineering of an idiotypic determinant.

A Tramontano, M Sollazzo, D Castiglia, 1990, Protein engineering.

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

Anna Tramontano, Fabio Cecconi, Carlo Guardiani, 2014, Journal of chemical theory and computation.

Further engineering of a designed protein, the minibody: from an insoluble to a soluble molecule

A. Tramontano, R. Bazzo, A. Pessi, 1994 .

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

Anna Tramontano, Jan Kosinski, Alessandro Barbato, 2013, Bioinform..

Ten Simple Rules for Developing a Short Bioinformatics Training Course

Anna Tramontano, Michelle D. Brazas, Javier De Las Rivas, 2011, PLoS Comput. Biol..

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

A. Tramontano, R. Lepore, M. Possenti, 2018, Scientific Reports.

Structural model and ligand interactions of the Xanthomonas axonopodis pv. citri oligopeptide-binding protein.

A. Tramontano, A. Giorgetti, L. Ferreira, 2007, Genetics and molecular research : GMR.

Endocytosis of synaptic ADAM 10 in neuronal plasticity and Alzheimer ’ s disease .

M. Giustetto, A. Tramontano, M. Luca, 2013 .

Critical assessment of methods of protein structure prediction (CASP)—Round 6

B. Rost, T. Hubbard, A. Tramontano, 2005, Proteins.

The protein folding problem: when will it be solved?

S Banu Ozkan, Vincent A Voelz, Ken A Dill, 2007, Current opinion in structural biology.

Conformational analysis of putative regulatory subunit D of the toluene/o‐xylene‐monooxygenase complex from Pseudomonas stutzeri OX1

A. Tramontano, P. Pucci, P. Barbieri, 2001, Protein science : a publication of the Protein Society.

GLASS: A tool to visualize protein structure prediction data in three dimensions and evaluate their consistency

R Leplae, T Hubbard, A Tramontano, 1998, Proteins.

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

A. Tramontano, A. Via, R. Lepore, 2012, Biochemical and biophysical research communications.

Redesigning the substrate specificity of the hepatitis C virus NS3 protease.

Failla, A. Tramontano, R. Francesco, 1996, Folding & design.

Exercise Training in Patients with Heart Failure: From Pathophysiology to Exercise Prescription

A. Tramontano, F. Giallauria, C. Vigorito, 2022, Reviews in cardiovascular medicine.

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

Anna Tramontano, Allegra Via, Rosalba Lepore, 2013, Bioinform..

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

Paolo Marcatili, Anna Tramontano, Rosalba Lepore, 2014, Bioinform..

Editorial

Dan Gusfield, Anna Tramontano, D. Gusfield, 2009, Bioinform..

The aim of the conference is to provide a scientific forum for discussing the issues and advances in computational biology.

A Tramontano, A. Tramontano, 2008, Bioinformatics.

Statistical evaluation of the coding capacity of complementary DNA strands.

A. Tramontano, M. Macchiato, V. Scarlato, 1984, Nucleic acids research.

The MEPS server for identifying protein conformational epitopes

Anna Tramontano, Massimiliano Orsini, Matteo Floris, 2007, BMC Bioinformatics.

Exploiting homology information in nontemplate based prediction of protein structures.

Anna Tramontano, Alfredo Iacoangeli, Paolo Marcatili, 2015, Journal of chemical theory and computation.

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

A. Tramontano, K. Fidelis, J. Moult, 2016, Proteins.

Evaluation of the template‐based modeling in CASP12

A. Tramontano, K. Fidelis, J. Moult, 2018, Proteins.

Critical assessment of methods of protein structure prediction—Round VIII

B. Rost, A. Tramontano, K. Fidelis, 2009, Proteins.

Evaluation of template‐based models in CASP8 with standard measures

B. Rost, D. Cozzetto, A. Tramontano, 2009, Proteins.

PIGS: automatic prediction of antibody structures

A. Tramontano, P. Marcatili, A. Rosi, 2008, Bioinform..

Cloning, characterization, and modeling of a monoclonal anti‐human transferrin antibody that competes with the transferrin receptor

A Tramontano, A. Tramontano, A. Santucci, 1994, Protein science : a publication of the Protein Society.

DeTECTOR: GENE TRANSLATION IN EUKARYOTES, A DIAGNOSTIC TOOL

A. Tramontano, M. Orsini, Silvano Salaris, 2009 .

Protein structure prediction

A. Tramontano, 2013 .

Comparative Modelling Techniques: Where are we?

Anna Tramontano, A. Tramontano, 2003, Comparative and functional genomics.

A statistical method for predicting alpha-helical and beta-sheet regions in proteins from their amino acidic sequences

A. Tramontano, V. Cuomo, M. Macchiato, 1984 .

The Evaluation of Protein Structure Prediction Results

Anna Tramontano, Domenico Raimondo, Domenico Cozzetto, 2008, Molecular biotechnology.

Structural Bioinformatics Prediction of the permeability of neutral drugs inferred from their solvation properties

A. Tramontano, D. Raimondo, E. Milanetti, 2016 .

The Aquila Digital Community The Aquila Digital Community

Silvio C. E. Tosatto, Karin M. Verspoor, David A. Lee, 2022 .

Evaluation of CASP8 model quality predictions

Anna Tramontano, Domenico Cozzetto, Andriy Kryshtafovych, 2009, Proteins.

Evaluation of protein structure prediction methods: Issues and strategies

Anna Tramontano, Domenico Cozzetto, D. Cozzetto, 2011 .

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

A. Tramontano, F. Facchinetti, L. Lugli, 2020, Minerva ginecologica.

Tabhu: tools for antibody humanization

Anna Tramontano, Pier Paolo Olimpieri, Paolo Marcatili, 2014, Bioinform..