Antibody-protein interactions: benchmark datasets and prediction tools evaluation.

PubWeight™: 2.14‹?› | Rank: Top 2%

🔗 View Article (PMC 2174481)

Published in BMC Struct Biol on October 02, 2007

Authors

Julia V Ponomarenko1, Philip E Bourne

Author Affiliations

1: San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. jpon@sdsc.edu

Articles citing this

ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics (2008) 2.26

Immune epitope database analysis resource. Nucleic Acids Res (2012) 2.09

Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics (2009) 1.55

DARS (Decoys As the Reference State) potentials for protein-protein docking. Biophys J (2008) 1.50

Identification of conformational B-cell Epitopes in an antigen from its primary sequence. Immunome Res (2010) 1.45

Computer-aided antibody design. Protein Eng Des Sel (2012) 1.44

Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Comput Biol (2012) 1.44

SEPPA: a computational server for spatial epitope prediction of protein antigens. Nucleic Acids Res (2009) 1.42

RosettaAntibody: antibody variable region homology modeling server. Nucleic Acids Res (2009) 1.35

Recent advances in B-cell epitope prediction methods. Immunome Res (2010) 1.26

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics (2010) 1.21

Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature. BMC Bioinformatics (2011) 1.20

Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis. BMC Bioinformatics (2008) 1.15

The structural basis of antibody-antigen recognition. Front Immunol (2013) 1.14

Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinformatics (2009) 1.12

Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics (2012) 1.08

Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods. PLoS One (2013) 1.07

Extensive antibody cross-reactivity among infectious gram-negative bacteria revealed by proteome microarray analysis. Mol Cell Proteomics (2008) 1.05

Potent adjuvanticity of a pure TLR7-agonistic imidazoquinoline dendrimer. PLoS One (2012) 1.04

Designing immunogenic peptides. Nat Chem Biol (2013) 0.99

High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics (2010) 0.97

Computer aided selection of candidate vaccine antigens. Immunome Res (2010) 0.95

Mining for the antibody-antigen interacting associations that predict the B cell epitopes. BMC Struct Biol (2010) 0.95

Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping. Biophys J (2010) 0.95

Computational docking of antibody-antigen complexes, opportunities and pitfalls illustrated by influenza hemagglutinin. Int J Mol Sci (2011) 0.93

Bioinformatics resources and tools for conformational B-cell epitope prediction. Comput Math Methods Med (2013) 0.92

Prediction of B-cell epitopes using evolutionary information and propensity scales. BMC Bioinformatics (2013) 0.91

Which clustering algorithm is better for predicting protein complexes? BMC Res Notes (2011) 0.90

New species of Ehrlichia isolated from Rhipicephalus (Boophilus) microplus shows an ortholog of the E. canis major immunogenic glycoprotein gp36 with a new sequence of tandem repeats. Parasit Vectors (2012) 0.90

A structural-alphabet-based strategy for finding structural motifs across protein families. Nucleic Acids Res (2010) 0.90

Common physical basis of macromolecule-binding sites in proteins. Nucleic Acids Res (2008) 0.87

SEPPA 2.0--more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen. Nucleic Acids Res (2014) 0.86

Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. BMC Bioinformatics (2013) 0.85

An analysis of B-cell epitope discontinuity. Mol Immunol (2012) 0.85

T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges. Immunome Res (2010) 0.84

B-Pred, a structure based B-cell epitopes prediction server. Adv Appl Bioinform Chem (2012) 0.82

B-cell epitope prediction through a graph model. BMC Bioinformatics (2012) 0.81

Tertiary structure-based prediction of conformational B-cell epitopes through B factors. Bioinformatics (2014) 0.81

Algorithmic approaches to protein-protein interaction site prediction. Algorithms Mol Biol (2015) 0.81

Epitope Recognition in the Human-Pig Comparison Model on Fixed and Embedded Material. J Histochem Cytochem (2015) 0.80

Antibody specific epitope prediction-emergence of a new paradigm. Curr Opin Virol (2015) 0.78

Conformational B-cell epitope prediction method based on antigen preprocessing and mimotopes analysis. Biomed Res Int (2015) 0.78

PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes. Nucleic Acids Res (2011) 0.78

The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design. Front Immunol (2017) 0.77

Peptide-based immunotherapeutics and vaccines. J Immunol Res (2014) 0.77

Prediction of peptide reactivity with human IVIg through a knowledge-based approach. PLoS One (2011) 0.77

Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates. Proteomes (2016) 0.77

Validation of glypican-3-specific scFv isolated from paired display/secretory yeast display library. BMC Biotechnol (2012) 0.76

Inadequate Reference Datasets Biased toward Short Non-epitopes Confound B-cell Epitope Prediction. J Biol Chem (2016) 0.75

Classification epitopes in groups based on their protein family. BMC Bioinformatics (2015) 0.75

Modeling and docking of antibody structures with Rosetta. Nat Protoc (2017) 0.75

Articles cited by this

The Protein Data Bank. Nucleic Acids Res (2000) 187.10

Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol (1978) 33.47

Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A (1981) 32.98

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng (1998) 28.09

Principles of protein-protein interactions. Proc Natl Acad Sci U S A (1996) 14.51

The atomic structure of protein-protein recognition sites. J Mol Biol (1999) 12.63

Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry (1974) 12.07

The Universal Protein Resource (UniProt). Nucleic Acids Res (2006) 11.50

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res (2005) 10.60

ZDOCK: an initial-stage protein-docking algorithm. Proteins (2003) 7.52

The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci U S A (1984) 6.36

ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics (2004) 6.04

Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol (1985) 5.73

Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120. Proc Natl Acad Sci U S A (2004) 5.15

Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution. Science (1986) 4.94

Improved method for predicting linear B-cell epitopes. Immunome Res (2006) 4.32

The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein. Nature (1984) 4.05

Conformational preferences of amino acids in globular proteins. Biochemistry (1978) 4.00

Correlation between segmental mobility and the location of antigenic determinants in proteins. Nature (1984) 3.66

Protein docking using continuum electrostatics and geometric fit. Protein Eng (2001) 3.48

Diversity of protein-protein interactions. EMBO J (2003) 3.35

Epitopes on protein antigens: misconceptions and realities. Cell (1990) 3.32

ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol (2004) 3.18

Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins (2006) 3.15

Comparison of a structural and a functional epitope. J Mol Biol (1993) 3.12

Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci (2006) 3.06

The design and implementation of the immune epitope database and analysis resource. Immunogenetics (2005) 3.00

Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics (2004) 2.93

Prediction of protein-protein interaction sites using patch analysis. J Mol Biol (1997) 2.91

Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci (2004) 2.70

On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. Biochemistry (1989) 2.56

Location of 'continuous' antigenic determinants in the protruding regions of proteins. EMBO J (1986) 2.22

CEP: a conformational epitope prediction server. Nucleic Acids Res (2005) 2.14

Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains). Proc Natl Acad Sci U S A (1986) 2.13

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit (2007) 2.02

Structural evidence for recognition of a single epitope by two distinct antibodies. Proteins (2000) 1.99

Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins (2003) 1.95

Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol Lett (1993) 1.65

Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity Methods (1996) 1.63

Structural and functional approaches to the study of protein antigenicity. Immunol Today (1989) 1.43

Machine learning approaches for prediction of linear B-cell epitopes on proteins. J Mol Recognit (2006) 1.41

Prediction of three-dimensional structure and mapping of conformational epitopes of envelope glycoprotein of Japanese encephalitis virus. Virology (1999) 1.29

PIER: protein interface recognition for structural proteomics. Proteins (2007) 1.22

Harnessing bioinformatics to discover new vaccines. Drug Discov Today (2007) 1.22

Mutagenesis-based definitions and probes of residue burial in proteins. Proc Natl Acad Sci U S A (2005) 1.17

Protein antigenicity: a thermodynamic approach. Mol Immunol (1991) 1.16

Synthetic peptides for the immunodiagnosis of human diseases. Curr Med Chem (2007) 1.15

EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). Immunome Res (2007) 1.10

Immunoinformatics may lead to a reappraisal of the nature of B cell epitopes and of the feasibility of synthetic peptide vaccines. J Mol Recognit (2006) 1.07

Autoantibodies to intracellular autoantigens and their B-cell epitopes: molecular probes to study the autoimmune response. Crit Rev Clin Lab Sci (2006) 1.00

Site-Directed Mutagenesis in Epitope Mapping Methods (1996) 0.96

Design of synthetic peptides for diagnostics. Curr Protein Pept Sci (2003) 0.88

Selection and combination of machine learning classifiers for prediction of linear B-cell epitopes on proteins. J Mol Recognit (2006) 0.87

Synthetic peptides as diagnostic tools in virology. Adv Virus Res (1993) 0.87

Current status of short synthetic peptides as vaccines. Med Chem (2006) 0.86

Old and new vaccine approaches. Int Immunopharmacol (2003) 0.82

Do we have suitable in-vitro diagnostic tests for the diagnosis of food allergy? Curr Opin Allergy Clin Immunol (2004) 0.78

Articles by these authors

(truncated to the top 100)

The Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2002) 14.44

The Protein Data Bank: unifying the archive. Nucleic Acids Res (2002) 12.37

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res (2005) 7.81

The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68

Ten simple rules for getting published. PLoS Comput Biol (2005) 7.22

The RCSB PDB information portal for structural genomics. Nucleic Acids Res (2006) 6.36

The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res (2012) 5.73

BioLit: integrating biological literature with databases. Nucleic Acids Res (2008) 4.85

SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82

Ten simple rules for getting grants. PLoS Comput Biol (2006) 3.13

Ten simple rules for a successful collaboration. PLoS Comput Biol (2007) 3.12

BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics (2012) 2.94

Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLoS Comput Biol (2009) 2.84

The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics (2005) 2.60

Ten simple rules for making good oral presentations. PLoS Comput Biol (2007) 2.57

Structural evolution of the protein kinase-like superfamily. PLoS Comput Biol (2005) 2.48

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A (2008) 2.44

Phylogeny determined by protein domain content. Proc Natl Acad Sci U S A (2005) 2.37

Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput Biol (2009) 2.35

Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32

Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir. PLoS Comput Biol (2011) 2.31

Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics (2010) 2.28

ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics (2008) 2.26

Open access: taking full advantage of the content. PLoS Comput Biol (2008) 2.14

Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14

Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proc Natl Acad Sci U S A (2006) 2.10

Immune epitope database analysis resource. Nucleic Acids Res (2012) 2.09

The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol (2010) 2.07

Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol (2005) 2.04

An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics (2002) 1.97

Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol (2010) 1.97

Biodiversity data should be published, cited, and peer reviewed. Trends Ecol Evol (2013) 1.97

Ten simple rules for reviewers. PLoS Comput Biol (2006) 1.84

Ten simple rules for selecting a postdoctoral position. PLoS Comput Biol (2006) 1.77

Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu Rev Pharmacol Toxicol (2011) 1.76

History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc Natl Acad Sci U S A (2010) 1.71

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics (2007) 1.70

PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res (2010) 1.69

Computational biology resources lack persistence and usability. PLoS Comput Biol (2008) 1.65

CE-MC: a multiple protein structure alignment server. Nucleic Acids Res (2004) 1.64

Topic pages: PLoS Computational Biology meets Wikipedia. PLoS Comput Biol (2012) 1.60

Quantifying reproducibility in computational biology: the case of the tuberculosis drugome. PLoS One (2013) 1.56

Ten simple rules for a good poster presentation. PLoS Comput Biol (2007) 1.55

Partitioning protein structures into domains: why is it so difficult? J Mol Biol (2006) 1.51

Biocurators: contributors to the world of science. PLoS Comput Biol (2006) 1.46

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics (2009) 1.46

Toward consistent assignment of structural domains in proteins. J Mol Biol (2004) 1.42

In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol (2007) 1.40

Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput (2008) 1.40

Ten simple rules for starting a company. PLoS Comput Biol (2012) 1.39

Curation of complex, context-dependent immunological data. BMC Bioinformatics (2006) 1.36

Teaching bioinformatics at the secondary school level. PLoS Comput Biol (2011) 1.34

Ten simple rules for doing your best research, according to Hamming. PLoS Comput Biol (2007) 1.32

Superimpose: a 3D structural superposition server. Nucleic Acids Res (2008) 1.31

SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res (2011) 1.29

Ten simple rules for organizing a scientific meeting. PLoS Comput Biol (2008) 1.26

Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol (2011) 1.25

Integration of open access literature into the RCSB Protein Data Bank using BioLit. BMC Bioinformatics (2010) 1.22

A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol (2010) 1.19

A biologist's guide to synchrotron facilities: the BioSync web resource. Trends Biochem Sci (2002) 1.15

An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. Immunome Res (2005) 1.15

Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins (2006) 1.14

EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). Immunome Res (2007) 1.10

The evolutionary history of protein domains viewed by species phylogeny. PLoS One (2009) 1.09

Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol (2009) 1.07

Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics (2006) 1.05

Ten simple rules for graduate students. PLoS Comput Biol (2007) 1.04

Wiggle-predicting functionally flexible regions from primary sequence. PLoS Comput Biol (2006) 1.03

A machine learning-based method to improve docking scoring functions and its application to drug repurposing. J Chem Inf Model (2011) 1.03

Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. Biol Direct (2009) 1.01

SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Res (2010) 1.00

Statistically rigorous automated protein annotation. Bioinformatics (2004) 0.97

Institutional Profile: University of California San Diego Pharmacogenomics Education Program (PharmGenEd™): bridging the gap between science and practice. Pharmacogenomics (2011) 0.94

TRANSLATING BIOLOGY: TEXT MINING TOOLS THAT WORK. Pac Symp Biocomput (2008) 0.94

What Big Data means to me. J Am Med Inform Assoc (2014) 0.94

Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology. Proteins (2005) 0.93

IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res (2010) 0.93

Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PLoS One (2010) 0.92

A comparative proteomics resource: proteins of Arabidopsis thaliana. Genome Biol (2003) 0.92

PLoS Computational Biology conference postcards from PSB 2010. PLoS Comput Biol (2010) 0.92

dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. BMC Bioinformatics (2010) 0.91

Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence. Int J Antimicrob Agents (2012) 0.90

Realism about PDB. Nat Biotechnol (2007) 0.89

Peptide identification by database search of mixture tandem mass spectra. Mol Cell Proteomics (2011) 0.88

Ten simple rules for cultivating open science and collaborative R&D. PLoS Comput Biol (2013) 0.88

Cobweb: a Java applet for network exploration and visualisation. Bioinformatics (2011) 0.88

A new scoring function and associated statistical significance for structure alignment by CE. J Comput Biol (2004) 0.88

High-throughput identification of interacting protein-protein binding sites. BMC Bioinformatics (2007) 0.88

Rethinking proteasome evolution: two novel bacterial proteasomes. J Mol Evol (2008) 0.87

Ten simple rules to combine teaching and research. PLoS Comput Biol (2009) 0.86

Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst Biol (2013) 0.86

Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2. BMC Bioinformatics (2007) 0.84

Building an automated classification of DNA-binding protein domains. Bioinformatics (2002) 0.84

Con-Struct Map: a comparative contact map analysis tool. Bioinformatics (2007) 0.84

CKAAPs DB: a Conserved Key Amino Acid Positions DataBase. Nucleic Acids Res (2002) 0.84

Conserved motifs in voltage-sensing and pore-forming modules of voltage-gated ion channel proteins. Biochem Biophys Res Commun (2006) 0.84

Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia. BMC Genomics (2013) 0.83

Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome. PLoS Comput Biol (2009) 0.83

Ten simple rules for chairing a scientific session. PLoS Comput Biol (2009) 0.82

Multipolar representation of protein structure. BMC Bioinformatics (2006) 0.81