Julia V Ponomarenko, Philip E Bourne. BMC Struct Biol 2007
Times Cited: 137
Times Cited: 137
Times Cited
Times Co-cited
Similarity
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures.
Pernille Haste Andersen, Morten Nielsen, Ole Lund. Protein Sci 2006
Pernille Haste Andersen, Morten Nielsen, Ole Lund. Protein Sci 2006
42
ElliPro: a new structure-based tool for the prediction of antibody epitopes.
Julia Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E Bourne, Alessandro Sette, Bjoern Peters. BMC Bioinformatics 2008
Julia Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E Bourne, Alessandro Sette, Bjoern Peters. BMC Bioinformatics 2008
37
Improved method for predicting linear B-cell epitopes.
Jens Erik Pontoppidan Larsen, Ole Lund, Morten Nielsen. Immunome Res 2006
Jens Erik Pontoppidan Larsen, Ole Lund, Morten Nielsen. Immunome Res 2006
34
Benchmarking B cell epitope prediction: underperformance of existing methods.
Martin J Blythe, Darren R Flower. Protein Sci 2005
Martin J Blythe, Darren R Flower. Protein Sci 2005
31
New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites.
J M Parker, D Guo, R S Hodges. Biochemistry 1986
J M Parker, D Guo, R S Hodges. Biochemistry 1986
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A semi-empirical method for prediction of antigenic determinants on protein antigens.
A S Kolaskar, P C Tongaonkar. FEBS Lett 1990
A S Kolaskar, P C Tongaonkar. FEBS Lett 1990
23
Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools.
Jason A Greenbaum, Pernille Haste Andersen, Martin Blythe, Huynh-Hoa Bui, Raul E Cachau, James Crowe, Matthew Davies, A S Kolaskar, Ole Lund, Sherrie Morrison,[...]. J Mol Recognit 2007
Jason A Greenbaum, Pernille Haste Andersen, Martin Blythe, Huynh-Hoa Bui, Raul E Cachau, James Crowe, Matthew Davies, A S Kolaskar, Ole Lund, Sherrie Morrison,[...]. J Mol Recognit 2007
23
Prediction of protein antigenic determinants from amino acid sequences.
T P Hopp, K R Woods. Proc Natl Acad Sci U S A 1981
T P Hopp, K R Woods. Proc Natl Acad Sci U S A 1981
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Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide.
E A Emini, J V Hughes, D S Perlow, J Boger. J Virol 1985
E A Emini, J V Hughes, D S Perlow, J Boger. J Virol 1985
20
Prediction of continuous B-cell epitopes in an antigen using recurrent neural network.
Sudipto Saha, G P S Raghava. Proteins 2006
Sudipto Saha, G P S Raghava. Proteins 2006
20
PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure.
Michael J Sweredoski, Pierre Baldi. Bioinformatics 2008
Michael J Sweredoski, Pierre Baldi. Bioinformatics 2008
19
CEP: a conformational epitope prediction server.
Urmila Kulkarni-Kale, Shriram Bhosle, A S Kolaskar. Nucleic Acids Res 2005
Urmila Kulkarni-Kale, Shriram Bhosle, A S Kolaskar. Nucleic Acids Res 2005
19
Predicting linear B-cell epitopes using string kernels.
Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar. J Mol Recognit 2008
Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar. J Mol Recognit 2008
18
Reliable B cell epitope predictions: impacts of method development and improved benchmarking.
Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, Morten Nielsen. PLoS Comput Biol 2012
Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, Morten Nielsen. PLoS Comput Biol 2012
18
Epitopia: a web-server for predicting B-cell epitopes.
Nimrod D Rubinstein, Itay Mayrose, Eric Martz, Tal Pupko. BMC Bioinformatics 2009
Nimrod D Rubinstein, Itay Mayrose, Eric Martz, Tal Pupko. BMC Bioinformatics 2009
17
SEPPA: a computational server for spatial epitope prediction of protein antigens.
Jing Sun, Di Wu, Tianlei Xu, Xiaojing Wang, Xiaolian Xu, Lin Tao, Y X Li, Z W Cao. Nucleic Acids Res 2009
Jing Sun, Di Wu, Tianlei Xu, Xiaojing Wang, Xiaolian Xu, Lin Tao, Y X Li, Z W Cao. Nucleic Acids Res 2009
17
Structural analysis of B-cell epitopes in antibody:protein complexes.
Jens Vindahl Kringelum, Morten Nielsen, Søren Berg Padkjær, Ole Lund. Mol Immunol 2013
Jens Vindahl Kringelum, Morten Nielsen, Søren Berg Padkjær, Ole Lund. Mol Immunol 2013
17
The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
16
Identification of conformational B-cell Epitopes in an antigen from its primary sequence.
Hifzur Rahman Ansari, Gajendra Ps Raghava. Immunome Res 2010
Hifzur Rahman Ansari, Gajendra Ps Raghava. Immunome Res 2010
15
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes.
Martin Closter Jespersen, Bjoern Peters, Morten Nielsen, Paolo Marcatili. Nucleic Acids Res 2017
Martin Closter Jespersen, Bjoern Peters, Morten Nielsen, Paolo Marcatili. Nucleic Acids Res 2017
15
Recent advances in B-cell epitope prediction methods.
Yasser El-Manzalawy, Vasant Honavar. Immunome Res 2010
Yasser El-Manzalawy, Vasant Honavar. Immunome Res 2010
14
Correlation between the location of antigenic sites and the prediction of turns in proteins.
J L Pellequer, E Westhof, M H Van Regenmortel. Immunol Lett 1993
J L Pellequer, E Westhof, M H Van Regenmortel. Immunol Lett 1993
14
Prediction of linear B-cell epitopes using amino acid pair antigenicity scale.
J Chen, H Liu, J Yang, K-C Chou. Amino Acids 2007
J Chen, H Liu, J Yang, K-C Chou. Amino Acids 2007
14
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results.
Shide Liang, Dandan Zheng, Daron M Standley, Bo Yao, Martin Zacharias, Chi Zhang. BMC Bioinformatics 2010
Shide Liang, Dandan Zheng, Daron M Standley, Bo Yao, Martin Zacharias, Chi Zhang. BMC Bioinformatics 2010
15
Prediction of antigenic epitopes on protein surfaces by consensus scoring.
Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias. BMC Bioinformatics 2009
Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias. BMC Bioinformatics 2009
18
Computational characterization of B-cell epitopes.
Nimrod D Rubinstein, Itay Mayrose, Dan Halperin, Daniel Yekutieli, Jonathan M Gershoni, Tal Pupko. Mol Immunol 2008
Nimrod D Rubinstein, Itay Mayrose, Dan Halperin, Daniel Yekutieli, Jonathan M Gershoni, Tal Pupko. Mol Immunol 2008
11
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.
Morten Nielsen, Claus Lundegaard, Peder Worning, Sanne Lise Lauemøller, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund. Protein Sci 2003
Morten Nielsen, Claus Lundegaard, Peder Worning, Sanne Lise Lauemøller, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund. Protein Sci 2003
11
Continuous and discontinuous protein antigenic determinants.
D J Barlow, M S Edwards, J M Thornton. Nature 1986
D J Barlow, M S Edwards, J M Thornton. Nature 1986
11
A machine-learning approach for predicting B-cell epitopes.
Nimrod D Rubinstein, Itay Mayrose, Tal Pupko. Mol Immunol 2009
Nimrod D Rubinstein, Itay Mayrose, Tal Pupko. Mol Immunol 2009
14
Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods.
Bo Yao, Dandan Zheng, Shide Liang, Chi Zhang. PLoS One 2013
Bo Yao, Dandan Zheng, Shide Liang, Chi Zhang. PLoS One 2013
15
Improving B-cell epitope prediction and its application to global antibody-antigen docking.
Konrad Krawczyk, Xiaofeng Liu, Terry Baker, Jiye Shi, Charlotte M Deane. Bioinformatics 2014
Konrad Krawczyk, Xiaofeng Liu, Terry Baker, Jiye Shi, Charlotte M Deane. Bioinformatics 2014
13
The immune epitope database (IEDB) 3.0.
Randi Vita, James A Overton, Jason A Greenbaum, Julia Ponomarenko, Jason D Clark, Jason R Cantrell, Daniel K Wheeler, Joseph L Gabbard, Deborah Hix, Alessandro Sette,[...]. Nucleic Acids Res 2015
Randi Vita, James A Overton, Jason A Greenbaum, Julia Ponomarenko, Jason D Clark, Jason R Cantrell, Daniel K Wheeler, Joseph L Gabbard, Deborah Hix, Alessandro Sette,[...]. Nucleic Acids Res 2015
11
Immune epitope database analysis resource.
Yohan Kim, Julia Ponomarenko, Zhanyang Zhu, Dorjee Tamang, Peng Wang, Jason Greenbaum, Claus Lundegaard, Alessandro Sette, Ole Lund, Philip E Bourne,[...]. Nucleic Acids Res 2012
Yohan Kim, Julia Ponomarenko, Zhanyang Zhu, Dorjee Tamang, Peng Wang, Jason Greenbaum, Claus Lundegaard, Alessandro Sette, Ole Lund, Philip E Bourne,[...]. Nucleic Acids Res 2012
11
17
Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature.
Wen Zhang, Yi Xiong, Meng Zhao, Hua Zou, Xinghuo Ye, Juan Liu. BMC Bioinformatics 2011
Wen Zhang, Yi Xiong, Meng Zhao, Hua Zou, Xinghuo Ye, Juan Liu. BMC Bioinformatics 2011
16
Prediction of the secondary structure of proteins from their amino acid sequence.
P Y Chou, G D Fasman. Adv Enzymol Relat Areas Mol Biol 1978
P Y Chou, G D Fasman. Adv Enzymol Relat Areas Mol Biol 1978
9
Location of 'continuous' antigenic determinants in the protruding regions of proteins.
J M Thornton, M S Edwards, W R Taylor, D J Barlow. EMBO J 1986
J M Thornton, M S Edwards, W R Taylor, D J Barlow. EMBO J 1986
9
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method.
Bjoern Peters, Alessandro Sette. BMC Bioinformatics 2005
Bjoern Peters, Alessandro Sette. BMC Bioinformatics 2005
9
Antibody-antigen interactions: contact analysis and binding site topography.
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R M MacCallum, A C Martin, J M Thornton. J Mol Biol 1996
9
SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models.
Aroop Sircar, Jeffrey J Gray. PLoS Comput Biol 2010
Aroop Sircar, Jeffrey J Gray. PLoS Comput Biol 2010
9
The immune epitope database 2.0.
Randi Vita, Laura Zarebski, Jason A Greenbaum, Hussein Emami, Ilka Hoof, Nima Salimi, Rohini Damle, Alessandro Sette, Bjoern Peters. Nucleic Acids Res 2010
Randi Vita, Laura Zarebski, Jason A Greenbaum, Hussein Emami, Ilka Hoof, Nima Salimi, Rohini Damle, Alessandro Sette, Bjoern Peters. Nucleic Acids Res 2010
9
An introduction to epitope prediction methods and software.
Xingdong Yang, Xinglong Yu. Rev Med Virol 2009
Xingdong Yang, Xinglong Yu. Rev Med Virol 2009
9
The atomic structure of protein-protein recognition sites.
L Lo Conte, C Chothia, J Janin. J Mol Biol 1999
L Lo Conte, C Chothia, J Janin. J Mol Biol 1999
9
A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach.
Peng Wang, John Sidney, Courtney Dow, Bianca Mothé, Alessandro Sette, Bjoern Peters. PLoS Comput Biol 2008
Peng Wang, John Sidney, Courtney Dow, Bianca Mothé, Alessandro Sette, Bjoern Peters. PLoS Comput Biol 2008
9
The antigenic structure of proteins: a reappraisal.
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9
Mining for the antibody-antigen interacting associations that predict the B cell epitopes.
Liang Zhao, Jinyan Li. BMC Struct Biol 2010
Liang Zhao, Jinyan Li. BMC Struct Biol 2010
20
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
Weizhong Li, Adam Godzik. Bioinformatics 2006
Weizhong Li, Adam Godzik. Bioinformatics 2006
9
Predictive estimation of protein linear epitopes by using the program PEOPLE.
A J Alix. Vaccine 1999
A J Alix. Vaccine 1999
9
VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines.
Irini A Doytchinova, Darren R Flower. BMC Bioinformatics 2007
Irini A Doytchinova, Darren R Flower. BMC Bioinformatics 2007
9
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11.
Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren Buus, Ole Lund, Morten Nielsen. Nucleic Acids Res 2008
Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren Buus, Ole Lund, Morten Nielsen. Nucleic Acids Res 2008
9
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.