A citation-based method for searching scientific literature

Julia V Ponomarenko, Philip E Bourne. BMC Struct Biol 2007
Times Cited: 137







List of co-cited articles
666 articles co-cited >1



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
372
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
660
37

Improved method for predicting linear B-cell epitopes.
Jens Erik Pontoppidan Larsen, Ole Lund, Morten Nielsen. Immunome Res 2006
740
34




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
159
23

Prediction of protein antigenic determinants from amino acid sequences.
T P Hopp, K R Woods. Proc Natl Acad Sci U S A 1981
21




CEP: a conformational epitope prediction server.
Urmila Kulkarni-Kale, Shriram Bhosle, A S Kolaskar. Nucleic Acids Res 2005
161
19

Predicting linear B-cell epitopes using string kernels.
Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar. J Mol Recognit 2008
436
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
359
18

Epitopia: a web-server for predicting B-cell epitopes.
Nimrod D Rubinstein, Itay Mayrose, Eric Martz, Tal Pupko. BMC Bioinformatics 2009
124
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
95
17

Structural analysis of B-cell epitopes in antibody:protein complexes.
Jens Vindahl Kringelum, Morten Nielsen, Søren Berg Padkjær, Ole Lund. Mol Immunol 2013
163
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
16


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
607
15

Recent advances in B-cell epitope prediction methods.
Yasser El-Manzalawy, Vasant Honavar. Immunome Res 2010
95
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
120
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
89
15

Prediction of antigenic epitopes on protein surfaces by consensus scoring.
Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias. BMC Bioinformatics 2009
65
18

Computational characterization of B-cell epitopes.
Nimrod D Rubinstein, Itay Mayrose, Dan Halperin, Daniel Yekutieli, Jonathan M Gershoni, Tal Pupko. Mol Immunol 2008
147
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
709
11

Continuous and discontinuous protein antigenic determinants.
D J Barlow, M S Edwards, J M Thornton. Nature 1986
436
11

A machine-learning approach for predicting B-cell epitopes.
Nimrod D Rubinstein, Itay Mayrose, Tal Pupko. Mol Immunol 2009
76
14


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
82
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
652
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
301
11

PREDITOP: a program for antigenicity prediction.
J L Pellequer, E Westhof. J Mol Graph 1993
56
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
61
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
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
223
9


Antibody-antigen interactions: contact analysis and binding site topography.
R M MacCallum, A C Martin, J M Thornton. J Mol Biol 1996
364
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
446
9

An introduction to epitope prediction methods and software.
Xingdong Yang, Xinglong Yu. Rev Med Virol 2009
115
9

The atomic structure of protein-protein recognition sites.
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
548
9

The antigenic structure of proteins: a reappraisal.
D C Benjamin, J A Berzofsky, I J East, F R Gurd, C Hannum, S J Leach, E Margoliash, J G Michael, A Miller, E M Prager. Annu Rev Immunol 1984
881
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
522
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.