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Antibody-protein interactions: benchmark datasets and prediction tools evaluation
Julia V Ponomarenko, Philip E Bourne
BMC Struct Biol. 2007; 7: 64. Published online 2007 October 2. doi: 10.1186/1472-6807-7-64
PMCID:
PMC2174481
Abstract Full Text PDF–1.0M Supplementary Material

Is Cited by the Following 23 Articles in this Archive:

Which clustering algorithm is better for predicting protein complexes?
Charalampos N Moschopoulos, Georgios A Pavlopoulos, Ernesto Iacucci, Jan Aerts, Spiridon Likothanassis, Reinhard Schneider, Sophia Kossida
BMC Res Notes. 2011; 4: 549. Published online 2011 December 20. doi: 10.1186/1756-0500-4-549
PMCID:
PMC3267700
Abstract Full Text PDF–389K Supplementary Material
Prediction of Peptide Reactivity with Human IVIg through a Knowledge-Based Approach
Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi
PLoS One. 2011; 6(8): e23616. Published online 2011 August 24. doi: 10.1371/journal.pone.0023616
Correction in:
PLoS One. 2011; 6(9): 10.1371/annotation/57a9c527-109a-435f-a78d-1b7bce0e578b.
PMCID:
PMC3160895
Abstract Full Text PDF–522K Supplementary Material Correction
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; 12: 341. Published online 2011 August 17. doi: 10.1186/1471-2105-12-341
PMCID:
PMC3228550
Abstract Full Text PDF–578K
PAComplex: a web server to infer peptide antigen families and binding models from TCR–pMHC complexes
I-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W254–W260. Published online 2011 June 11. doi: 10.1093/nar/gkr434
PMCID:
PMC3125798
Abstract Full Text PDF–6.4M
Computational Docking of Antibody-Antigen Complexes, Opportunities and Pitfalls Illustrated by Influenza Hemagglutinin
Mattia Pedotti, Luca Simonelli, Elsa Livoti, Luca Varani
Int J Mol Sci. 2011; 12(1): 226–251. Published online 2011 January 5. doi: 10.3390/ijms12010226
PMCID:
PMC3039950
Abstract Full Text PDF–771K
T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges
Darren R Flower, Kanchan Phadwal, Isabel K Macdonald, Peter V Coveney, Matthew N Davies, Shunzhou Wan
Immunome Res. 2010; 6(Suppl 2): S4. Published online 2010 November 3. doi: 10.1186/1745-7580-6-S2-S4
PMCID:
PMC2981876
Abstract Full Text PDF–575K
Recent advances in B-cell epitope prediction methods
Yasser EL-Manzalawy, Vasant Honavar
Immunome Res. 2010; 6(Suppl 2): S2. Published online 2010 November 3. doi: 10.1186/1745-7580-6-S2-S2
PMCID:
PMC2981878
Abstract Full Text PDF–279K
Computer aided selection of candidate vaccine antigens
Darren R Flower, Isabel K Macdonald, Kamna Ramakrishnan, Matthew N Davies, Irini A Doytchinova
Immunome Res. 2010; 6(Suppl 2): S1. Published online 2010 November 3. doi: 10.1186/1745-7580-6-S2-S1
PMCID:
PMC2981880
Abstract Full Text PDF–717K
Identification of conformational B-cell Epitopes in an antigen from its primary sequence
Hifzur Rahman Ansari, Gajendra PS Raghava
Immunome Res. 2010; 6: 6. Published online 2010 October 20. doi: 10.1186/1745-7580-6-6
PMCID:
PMC2974664
Abstract Full Text PDF–1.2M Supplementary Material
High-throughput prediction of protein antigenicity using protein microarray data
Christophe N. Magnan, Michael Zeller, Matthew A. Kayala, Adam Vigil, Arlo Randall, Philip L. Felgner, Pierre Baldi
Bioinformatics. 2010 December 1; 26(23): 2936–2943. Published online 2010 October 7. doi: 10.1093/bioinformatics/btq551
PMCID:
PMC2982151
Abstract Full Text PDF–190K Supplementary Material
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; 11: 381. Published online 2010 July 16. doi: 10.1186/1471-2105-11-381
PMCID:
PMC2910724
Abstract Full Text PDF–674K
A structural-alphabet-based strategy for finding structural motifs across protein families
Chih Yuan Wu, Yao Chi Chen, Carmay Lim
Nucleic Acids Res. 2010 August; 38(14): e150. Published online 2010 June 4. doi: 10.1093/nar/gkq478
PMCID:
PMC2919736
Abstract Full Text PDF–6.2M Supplementary Material
Mining for the antibody-antigen interacting associations that predict the B cell epitopes
Liang Zhao, Jinyan Li
BMC Struct Biol. 2010; 10(Suppl 1): S6. Published online 2010 May 17. doi: 10.1186/1472-6807-10-S1-S6
PMCID:
PMC2873829
Abstract Full Text PDF–1006K
Predicting Interaction Sites from the Energetics of Isolated Proteins: A New Approach to Epitope Mapping
Guido Scarabelli, Giulia Morra, Giorgio Colombo
Biophys J. 2010 May 5; 98(9): 1966–1975. doi: 10.1016/j.bpj.2010.01.014
PMCID:
PMC2862194
Abstract Full Text PDF–630K Supplementary Material
Prediction of antigenic epitopes on protein surfaces by consensus scoring
Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias
BMC Bioinformatics. 2009; 10: 302. Published online 2009 September 22. doi: 10.1186/1471-2105-10-302
PMCID:
PMC2761409
Abstract Full Text PDF–1.3M
Epitopia: a web-server for predicting B-cell epitopes
Nimrod D Rubinstein, Itay Mayrose, Eric Martz, Tal Pupko
BMC Bioinformatics. 2009; 10: 287. Published online 2009 September 14. doi: 10.1186/1471-2105-10-287
PMCID:
PMC2751785
Abstract Full Text PDF–566K
RosettaAntibody: antibody variable region homology modeling server
Aroop Sircar, Eric T. Kim, Jeffrey J. Gray
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W474–W479. Published online 2009 July 1. doi: 10.1093/nar/gkp387
PMCID:
PMC2703951
Abstract Full Text PDF–3.1M
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 July 1; 37(Web Server issue): W612–W616. Published online 2009 July 1. doi: 10.1093/nar/gkp417
PMCID:
PMC2703964
Abstract Full Text PDF–3.7M Supplementary Material
Extensive Antibody Cross-reactivity among Infectious Gram-negative Bacteria Revealed by Proteome Microarray Analysis
Sarah L. Keasey, Kara E. Schmid, Michael S. Lee, James Meegan, Patricio Tomas, Michael Minto, Alexander P. Tikhonov, Barry Schweitzer, Robert G. Ulrich
Mol Cell Proteomics. 2009 May; 8(5): 924–935. doi: 10.1074/mcp.M800213-MCP200
PMCID:
PMC2689768
Abstract Full Text
Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis
Yan Xin Huang, Yong Li Bao, Shu Yan Guo, Yan Wang, Chun Guang Zhou, Yu Xin Li
BMC Bioinformatics. 2008; 9: 538. Published online 2008 December 16. doi: 10.1186/1471-2105-9-538
PMCID:
PMC2639436
Abstract Full Text PDF–570K Supplementary Material
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; 9: 514. Published online 2008 December 2. doi: 10.1186/1471-2105-9-514
PMCID:
PMC2607291
Abstract Full Text PDF–2.0M Supplementary Material
Common physical basis of macromolecule-binding sites in proteins
Yao Chi Chen, Carmay Lim
Nucleic Acids Res. 2008 December; 36(22): 7078–7087. Published online 2008 December. doi: 10.1093/nar/gkn868
PMCID:
PMC2602788
Abstract Full Text PDF–1.3M Supplementary Material
DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking
Gwo-Yu Chuang, Dima Kozakov, Ryan Brenke, Stephen R. Comeau, Sandor Vajda
Biophys J. 2008 November 1; 95(9): 4217–4227. Published online 2008 August 1. doi: 10.1529/biophysj.108.135814
PMCID:
PMC2567923
Abstract Full Text PDF–319K Supplementary Material
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