Antibody-protein interactions: benchmark datasets and prediction tools evaluation (Q33301223)

25 July 2017

Antibody-protein interactions: benchmark datasets and prediction tools evaluation (English)

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25 July 2017

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2

Philip E Bourne

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Julia Ponomarenko

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object named as

Julia V Ponomarenko

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PubMed ID

17910770

25 July 2017

language of work or name

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2 October 2007

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25 July 2017

BMC Structural Biology

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25 July 2017

7

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25 July 2017

64

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https://scigraph.springernature.com/pub.10.1186/1472-6807-7-64

25 July 2017

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21 June 2018

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21 June 2018

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Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools

21 June 2018

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21 June 2018

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Current status of short synthetic peptides as vaccines

21 June 2018

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Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

21 June 2018

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Improved method for predicting linear B-cell epitopes

21 June 2018

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Machine learning approaches for prediction of linear B-cell epitopes on proteins

21 June 2018

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Autoantibodies to intracellular autoantigens and their B-cell epitopes: molecular probes to study the autoimmune response.

21 June 2018

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Mutagenesis-based definitions and probes of residue burial in proteins.

21 June 2018

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ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

21 June 2018

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CEP: a conformational epitope prediction server.

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

The design and implementation of the immune epitope database and analysis resource

21 June 2018

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Do we have suitable in-vitro diagnostic tests for the diagnosis of food allergy?

21 June 2018

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Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120

21 June 2018

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Design of Synthetic Peptides for Diagnostics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Old and new vaccine approaches

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Diversity of protein-protein interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Structural evidence for recognition of a single epitope by two distinct antibodies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

21 June 2018

The Protein Data Bank

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The atomic structure of protein-protein recognition sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Site-Directed Mutagenesis in Epitope Mapping

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Principles of protein-protein interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Synthetic peptides as diagnostic tools in virology.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

The hydrophobic moment detects periodicity in protein hydrophobicity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Correlation between segmental mobility and the location of antigenic determinants in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Prediction of protein antigenic determinants from amino acid sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Structural and functional approaches to the study of protein antigenicity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Location of 'continuous' antigenic determinants in the protruding regions of proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Epitopes on protein antigens: misconceptions and realities.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Conformational preferences of amino acids in globular proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Prediction of continuous B-cell epitopes in an antigen using recurrent neural network.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Selection and combination of machine learning classifiers for prediction of linear B-cell epitopes on proteins.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Improved prediction of protein-protein binding sites using a support vector machines approach.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Benchmarking B cell epitope prediction: underperformance of existing methods

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

ProMate: a structure based prediction program to identify the location of protein-protein binding sites

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

ClusPro: an automated docking and discrimination method for the prediction of protein complexes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

ZDOCK: an initial-stage protein-docking algorithm.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Prediction of three-dimensional structure and mapping of conformational epitopes of envelope glycoprotein of Japanese encephalitis virus

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Prediction of protein-protein interaction sites using patch analysis.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174481

Correlation between the location of antigenic sites and the prediction of turns in proteins

31 October 2018

1 reference

12 December 2020

Immunoinformatics may lead to a reappraisal of the nature of B cell epitopes and of the feasibility of synthetic peptide vaccines

1 reference

12 December 2020

Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution

1 reference

12 December 2020

Comparison of a structural and a functional epitope

1 reference

12 December 2020

Protein antigenicity: A thermodynamic approach

1 reference

12 December 2020

The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein

1 reference

12 December 2020

Protein docking using continuum electrostatics and geometric fit

1 reference

12 December 2020

Identifiers

DOI

10.1186/1472-6807-7-64

1 reference

PubMed ID

17910770

Dimensions Publication ID

25 July 2017

0 references

1 reference

25 July 2017

1 reference

PubMed ID

17910770