Search filters

Authors whose works are in public domain in at least one jurisdiction

List of works by Anna Tramontano

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

scientific article (publication date: June 2015)

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

scientific article (publication date: November 2011)

A brighter future for protein design

scientific article

A computational approach for the functional classification of the epigenome

scientific article published on 15 May 2017

A database of immunoglobulins with integrated tools: DIGIT

scientific article

A database system for handling phage library-derived sequences

scientific article published on June 1993

A designed metal-binding protein with a novel fold

scientific article published on March 1993

A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA

scientific article

A model for recognition of polychlorinated dibenzo‐p‐dioxins by the aryl hydrocarbon receptor ⬇️

scientific article published on January 1, 2002

A model for the hepatitis C virus envelope glycoprotein E2.

scientific article published in August 2000

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

scientific article published on November 2007

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

scientific article

A resource for benchmarking the usefulness of protein structure models ⬇️

scientific article (publication date: 2 August 2012)

A stereospecific cyclization catalyzed by an antibody

scientific article published in August 1987

A structural view of microRNA-target recognition

scientific article (publication date: 19 May 2016)

A structure-activity study of a catalytic antiidiotypic antibody to the human erythrocyte acetylcholinesterase

scientific article

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

scientific article

A transportable interactive package for the statistical analysis and handling of sequence data ⬇️

scientific article published on January 1, 1988

A zinc binding site in viral serine proteinases

scientific article published on October 1996

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

scientific article

Advances and pitfalls in protein structure prediction.

scientific article

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

scientific article published in July 1993

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

scientific article

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

scientific article

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

scientific article (publication date: 19 April 2006)

An automatic method for identifying surface proteins in bacteria: SLEP

scientific article (publication date: 20 January 2010)

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

scientific article

Analysis and assessment of comparative modeling predictions in CASP4.

scientific article

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

scientific article

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

scientific article

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

scientific article

Antibody modeling: implications for engineering and design.

scientific article

Antibody structure, prediction and redesign

scientific article

Assessment of homology-based predictions in CASP5.

scientific article

Assessment of model accuracy estimations in CASP12.

scientific article published on 17 August 2017

Assessment of predictions in the model quality assessment category.

scientific article

Assessment of protein disorder region predictions in CASP10

scientific article (publication date: February 2014)

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

scientific article (publication date: February 2014)

Automatic procedure for using models of proteins in molecular replacement.

scientific article

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

scientific article (publication date: 18 February 2000)

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.

scientific article

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

scientific article published on 8 December 2014

Cancer-selective targeting of the NF-κB survival pathway with GADD45β/MKK7 inhibitors

scientific article

Catalysis of esterolytic reactions by the anti-idiotypic antibody against human erythrocyte acetylcholinesterase

scientific article published on March 1, 2001

Catalytic antibodies

scientific article

Catalytic antibodies

scientific article published on 01 January 1987

Catalytic antibodies

scientific article published on 01 March 1988

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

scientific article (publication date: March 2015)

Chemical equilibrium at an antibody binding site: catalytic efficiency defined by a Haldane relationship

scientific article published in September 1990

Chemical reactivity at an antibody binding site elicited by mechanistic design of a synthetic antigen

scientific article published on September 1986

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

scientific article published in April 1993

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

scientific article

Clinical quiz. Long-segment Hirschsprung's disease (total colonic aganglionosis).

scientific article

Clinico-statistical study of third-trimester gestosis during the 5-year period of 1964-1968

scientific article published on August 1, 1971

Cloning and analysis of Candida cylindracea lipase sequences.

scientific article published in February 1993

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

scientific article

Coding potential of the products of alternative splicing in human

scientific article (publication date: 2011)

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

scientific article published in July 1992

Comparative modelling techniques: where are we?

scientific article (publication date: 2003)

Comparison of antibody and albumin catalyzed hydrolysis of steroidal p-nitrophenylcarbonates

scientific article

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

scientific article

Conformations of immunoglobulin hypervariable regions

scientific article

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

scientific article

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

scientific article published in March 2006

Correction for Ballarino et al., "Novel Long Noncoding RNAs (lncRNAs) in Myogenesis: a miR-31 Overlapping lncRNA Transcript Controls Myoblast Differentiation".

scientific article

Covalent binding antibodies suppress advanced glycation: on the innate tier of adaptive immunity.

scientific article

Critical assessment of methods of protein structure prediction (CASP)--round 6.

scientific article

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

scientific article (publication date: 2011)

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

scientific article (publication date: February 2014)

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

scientific article published on 30 October 2017

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

scientific article published in January 2009

Critical assessment of methods of protein structure prediction-Round VII

scientific article

DANTE: a workbench for sequence analysis

scientific article

Detecting mutually exclusive interactions in protein-protein interaction maps

scientific article

Detection of blood pressure increments in active elderly individuals: the role of ambulatory blood pressure monitoring

scientific article

Determination of the autocorrelation orders of proteins

scientific article published in June 1985

Differential capacity of anti-RAP and anti-megalin antibodies to produce progressive passive Heymann nephritis - implications for the pathogenesis of idiopathic human membranous glomerulonephritis

scientific article published in November 2006

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

scientific article published on 17 January 2015

Dissecting the structural determinants of the interaction between the human cytomegalovirus UL18 protein and the CD85j immune receptor

scientific article published on January 2008

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

scientific article published on 3 August 2017

Early treatment with ursodeoxycholic acid for cholestasis in children on parenteral nutrition because of primary intestinal failure

scientific article

Editorial

scientific article (publication date: 28 May 2009)

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

scientific article (publication date: June 2013)

Engineering stable cytoplasmic intrabodies with designed specificity

scientific article

Enzyme mimicry by the antiidiotypic antibody approach

scientific article

Epitope-specific antibody and suppression of autoantibody responses against a hybrid self protein.

scientific article

Erratum: antibody modeling using the Prediction of ImmunoGlobulin Structure (PIGS) web server

scientific article

Evaluating the usefulness of protein structure models for molecular replacement.

scientific article

Evaluation of CASP8 model quality predictions.

scientific article

Evaluation of annotation strategies using an entire genome sequence

scientific article

Evaluation of disorder predictions in CASP9

scientific article (publication date: 2011)

Evaluation of model quality predictions in CASP9

scientific article (publication date: 2011)

Evaluation of residue-residue contact prediction in CASP10

scientific article (publication date: February 2014)

Evaluation of residue-residue contact predictions in CASP9

scientific article (publication date: 2011)

Evaluation of template-based models in CASP8 with standard measures

scientific article (publication date: 2009)

Evaluation of the template-based modeling in CASP12.

scientific article

Evolution of bacterial and archaeal multicomponent monooxygenases

scientific article published in April 2003

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

scientific article published on July 20, 2011

Exploiting evolutionary relationships for predicting protein structures

scientific article published on December 2003

Exploiting homology information in nontemplate based prediction of protein structures.

scientific article

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

scientific article

Exploring the cytochrome c folding mechanism: cytochrome c552 from thermus thermophilus folds through an on-pathway intermediate

scientific article published on 2 July 2003

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

scientific article (publication date: July 2013)

Foker's technique in oesophageal atresia with double fistula: a case report

scientific article

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

scientific article published in September 1990

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

scientific article (publication date: 26 March 2008)

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

scientific article

Gathering them in to the fold

scientific article

Genome sequences and great expectations

scientific article

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

scientific article published in Scientific Reports

Genome-wide identification of direct HBx genomic targets

scientific article (publication date: 17 February 2017)

HBx–DLEU2 lncRNA complex affects transcription of new target promoters

Hepatitis C virus proteins as targets for drug development: the role of bioinformatics and modelling

scientific article

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

scientific article

Homology Modeling with Low Sequence Identity ⬇️

scientific article published on March 1, 1998

Homology-derived three-dimensional structure prediction of Candida cylindracea lipase

scientific article published in November 1992

Horizontal and vertical growth of S. cerevisiae metabolic network ⬇️

scientific article (publication date: 14 October 2011)

Human menopause gonadotropins in male deficiency of gonadostimulins

scientific article published on 01 September 1968

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

scientific article

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

scientific article

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

scientific article published on February 1995

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

scientific article published on 28 October 2011

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

scientific article published on April 1995

Immune recognition, antigen design, and catalytic antibody production

scientific article

Impact of antisecretory treatment on respiratory symptoms of gastroesophageal reflux disease in children

scientific article published on 11 January 2012

Impact of the Rome II paediatric criteria on the appropriateness of the upper and lower gastrointestinal endoscopy in children

scientific article published on 28 May 2010

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

scientific article (publication date: October 2014)

Improving your target-template alignment with MODalign

scientific article (publication date: April 2012)

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

scientific article published in January 2010

In vivo selection of protease cleavage sites by using chimeric Sindbis virus libraries

scientific article published in November 2000

Induction of cross-reactive humoral immune response by immunization with mimotopes of the hypervariable region 1 of the hepatitis C virus.

scientific article

Inhibition and labeling of enzymes and abzymes by phosphonate diesters

scientific article

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

scientific article published on 8 December 2011

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

scientific article (publication date: December 2015)

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

scientific article (publication date: 15 June 2011)

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

scientific article published on July 2015

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

scientific article (publication date: April 2013)

Mapping epitopes on protein surfaces.

scientific article

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

scientific article

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

scientific article (publication date: 26 February 2013)

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

scientific article

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

scientific article (publication date: September 2007)

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

scientific article published on June 15, 1993

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

scientific article

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

scientific article published on 31 August 2008

Modelling antibody-antigen interactions: ferritin as a case study

scientific article published on September 1995

Molecular cloning of a proteolytic antibody light chain

scientific article

Molecular cloning of a proteolytic antibody light chain.

scientific article published on December 1994

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

scientific article (publication date: 19 March 2011)

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

scientific article published on February 1994

Monoclonal antibody light chain with prothrombinase activity

scientific article

Multistep current signal in protein translocation through graphene nanopores

scientific article

Mutation pattern of paired immunoglobulin heavy and light variable domains in chronic lymphocytic leukemia B cells

scientific article (publication date: 2011)

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.

scientific article

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

scientific article published on 16 October 2015

No protein is an island

scientific article published on 30 May 2009

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

scientific article published on 4 March 2011

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

scientific article (publication date: February 2015)

Nucleophilic proteolytic antibodies

scientific article published in January 2000

Of men and machines

scientific article

On the mechanism of chloroquine resistance in Plasmodium falciparum

scientific article

PICMI: mapping point mutations on genomes

scientific article (publication date: 15 November 2010)

PIGS: automatic prediction of antibody structures

scientific article

PIGSPro: prediction of immunoGlobulin structures v2

scientific article

PLANET: a phage library analysis expert tool.

scientific article published on January 1995

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

scientific article

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

scientific article (publication date: 8 July 2016)

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

scientific article

Phosphonate ester probes for proteolytic antibodies

scientific article

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

scientific article (publication date: 15 September 2013)

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

scientific article (publication date: 15 April 2016)

ProCoCoA: A quantitative approach for analyzing protein core composition.

scientific article published on 31 December 2012

Probability of coding of a DNA sequence: an algorithm to predict translated reading frames from their thermodynamic characteristics

scientific article published on January 1986

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

scientific article

Production of antibodies that mimic enzyme catalytic activity

scientific article published in January 1989

Protein function annotation by homology-based inference

scientific article (publication date: 2 February 2009)

Protein structure prediction and design

scientific article

Protein structure prediction: playing the fold

scientific article

Proteolytic Antibodies: Origins, Selection and Induction ⬇️

scientific article published on January 1, 2000

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

scientific article

Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries

scientific article (publication date: 2014)

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

scientific article published on January 1998

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

scientific article published on January 1996

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

scientific article published in January 1995

Relationship between multiple sequence alignments and quality of protein comparative models.

scientific article

Remarkably similar antigen receptors among a subset of patients with chronic lymphocytic leukemia

scientific article (publication date: April 2004)

Remarkably similar antigen receptors among a subset of patients with chronic lymphocytic leukemia

Replacing the glutamate ligand in the structural zinc site of Sulfolobus solfataricus alcohol dehydrogenase with a cysteine decreases thermostability

scientific article published in January 1995

Revisiting the prediction of protein function at CASP6.

scientific article

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

scientific article

Screening Strategies for Catalytic Antitransition-State Analog Antibodies

scientific article published on January 1, 1995

Selection of functional variants of the NS3-NS4A protease of hepatitis C virus by using chimeric sindbis viruses

scientific article

Sequences and topology: the completeness of biological space

article published in 2007

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

scientific article

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

scientific article published on 16 October 2009

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

scientific article published on 27 February 2007

Spontaneous hydrolysis of vasoactive intestinal peptide in neutral aqueous solution.

scientific article

Statistical evaluation of the coding capacity of complementary DNA strands

scholarly article

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

scientific article (publication date: October 2010)

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

scientific article

Structural definition by antibody engineering of an idiotypic determinant

scientific article published on May 1990

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

scientific article published in January 1989

Structural repertoire of immunoglobulin λ light chains

scientific article published in March 2011

Substrate specificity of the hepatitis C virus serine protease NS3.

scientific article published in April 1997

Substrate-driven formation of a proteolytic antibody light chain.

scientific article

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

scientific article

Surface topology of Minibody by selective chemical modifications and mass spectrometry.

scientific article published on September 1997

Tabhu: tools for antibody humanization

scientific article (publication date: February 2015)

Temporal study of immunoglobin M seroreactivity to Borrelia burgdorferi in patients treated for Lyme borreliosis.

scientific article published on March 1997

Ten simple rules for developing a short bioinformatics training course

scientific article

Ten years of predictions ... and counting

scientific article

The Computational Analysis of Protein Structures: Sources, Methods, Systems and Results

scientific article (publication date: 1989)

The MEPS server for identifying protein conformational epitopes

scientific article (publication date: 8 March 2007)

The MoVIN server for the analysis of protein interaction networks

scientific article (publication date: 26 March 2008)

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

scientific article (publication date: 2013)

The PMDB Protein Model Database

scientific article

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

scientific article published on 25 July 2016

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

scientific article

The assessment of methods for protein structure prediction.

scientific article

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

scientific article (publication date: August 2011)

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

scientific article

The computational prediction of protein assemblies

scientific article published on 25 October 2017

The evaluation of protein structure prediction results.

scientific article

The implications of alternative splicing in the ENCODE protein complement

scientific article (publication date: 27 March 2007)

The making of the minibody: an engineered beta-protein for the display of conformationally constrained peptides

scientific article published on March 1994

The mepsMAP server. Mapping epitopes on protein surface: mining annotated proteins

scientific article

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

scientific article published on June 1997

The prediction of protein function at CASP6.

scientific article published on January 2005

The role of molecular modelling in biomedical research

scientific article

The significance of performance ranking in CASP--response to Marti-Renom et al.

scientific article

Thermodynamic approach to a possible theory of the evolution of a genetic code

scientific article published in October 1982

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

scientific article (publication date: 15 July 2013)

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

scientific article published on July 1, 1998

Treatment of Hirschsprung's disease with the Soave-Coran technique: experience with newborns and children

scientific article published on 01 January 1997

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

scientific article

VARIANT: a store and retrieval system for human haemoglobin variants

scientific article published in February 1990

Variability within the Candida rugosa lipases family

scientific article

Worth the effort. An account of the Seventh Meeting of the Worldwide Critical Assessment of Techniques for Protein Structure Prediction

scientific article

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

scientific article (publication date: February 2008)

[Biliary atresia syndrome and splenic malformation. A case report]

scientific article published on 01 August 2001

[Thyrotoxicosis in pregnancy and hepatic disturbances (new clinical and therapeutic orientations)]

scientific article published on 01 February 1965

Paulina is supported by:

About Paulina

Help