A citation-based method for searching scientific literature

Julia Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E Bourne, Alessandro Sette, Bjoern Peters. BMC Bioinformatics 2008
Times Cited: 660







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



Times Cited
  Times     Co-cited
Similarity





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
34

In silico approach for predicting toxicity of peptides and proteins.
Sudheer Gupta, Pallavi Kapoor, Kumardeep Chaudhary, Ankur Gautam, Rahul Kumar, Gajendra P S Raghava. PLoS One 2013
586
34


Designing of interferon-gamma inducing MHC class-II binders.
Sandeep Kumar Dhanda, Pooja Vir, Gajendra P S Raghava. Biol Direct 2013
289
26

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host.
Andreas Grote, Karsten Hiller, Maurice Scheer, Richard Münch, Bernd Nörtemann, Dietmar C Hempel, Dieter Jahn. Nucleic Acids Res 2005
651
26

The ClusPro web server for protein-protein docking.
Dima Kozakov, David R Hall, Bing Xia, Kathryn A Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda. Nat Protoc 2017
25

AllerTOP v.2--a server for in silico prediction of allergens.
Ivan Dimitrov, Ivan Bangov, Darren R Flower, Irini Doytchinova. J Mol Model 2014
321
23


AllergenFP: allergenicity prediction by descriptor fingerprints.
Ivan Dimitrov, Lyudmila Naneva, Irini Doytchinova, Ivan Bangov. Bioinformatics 2014
259
21

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction.
Mette V Larsen, Claus Lundegaard, Kasper Lamberth, Soren Buus, Ole Lund, Morten Nielsen. BMC Bioinformatics 2007
449
20

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
203
20

GalaxyRefine: Protein structure refinement driven by side-chain repacking.
Lim Heo, Hahnbeom Park, Chaok Seok. Nucleic Acids Res 2013
441
20

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
19

Predicting linear B-cell epitopes using string kernels.
Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar. J Mol Recognit 2008
436
19

The PSIPRED protein structure prediction server.
L J McGuffin, K Bryson, D T Jones. Bioinformatics 2000
17

SOLpro: accurate sequence-based prediction of protein solubility.
Christophe N Magnan, Arlo Randall, Pierre Baldi. Bioinformatics 2009
227
16

PatchDock and SymmDock: servers for rigid and symmetric docking.
Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J Wolfson. Nucleic Acids Res 2005
16

In-silico design of a multi-epitope vaccine candidate against onchocerciasis and related filarial diseases.
Robert Adamu Shey, Stephen Mbigha Ghogomu, Kevin Kum Esoh, Neba Derrick Nebangwa, Cabirou Mounchili Shintouo, Nkemngo Francis Nongley, Bertha Fru Asa, Ferdinand Njume Ngale, Luc Vanhamme, Jacob Souopgui. Sci Rep 2019
152
15

Properties of MHC class I presented peptides that enhance immunogenicity.
Jorg J A Calis, Matt Maybeno, Jason A Greenbaum, Daniela Weiskopf, Aruna D De Silva, Alessandro Sette, Can Keşmir, Bjoern Peters. PLoS Comput Biol 2013
392
15

Protein-Sol: a web tool for predicting protein solubility from sequence.
Max Hebditch, M Alejandro Carballo-Amador, Spyros Charonis, Robin Curtis, Jim Warwicker. Bioinformatics 2017
203
15


Prediction of IL4 inducing peptides.
Sandeep Kumar Dhanda, Sudheer Gupta, Pooja Vir, G P S Raghava. Clin Dev Immunol 2013
126
14

The PSIPRED Protein Analysis Workbench: 20 years on.
Daniel W A Buchan, David T Jones. Nucleic Acids Res 2019
556
14

iMODS: internal coordinates normal mode analysis server.
José Ramón López-Blanco, José I Aliaga, Enrique S Quintana-Ortí, Pablo Chacón. Nucleic Acids Res 2014
212
14


Improved methods for predicting peptide binding affinity to MHC class II molecules.
Kamilla Kjaergaard Jensen, Massimo Andreatta, Paolo Marcatili, Søren Buus, Jason A Greenbaum, Zhen Yan, Alessandro Sette, Bjoern Peters, Morten Nielsen. Immunology 2018
348
13


Peptide binding predictions for HLA DR, DP and DQ molecules.
Peng Wang, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund, Morten Nielsen, Bjoern Peters. BMC Bioinformatics 2010
406
13



Predicting population coverage of T-cell epitope-based diagnostics and vaccines.
Huynh-Hoa Bui, John Sidney, Kenny Dinh, Scott Southwood, Mark J Newman, Alessandro Sette. BMC Bioinformatics 2006
350
13

A candidate multi-epitope vaccine against SARS-CoV-2.
Tamalika Kar, Utkarsh Narsaria, Srijita Basak, Debashrito Deb, Filippo Castiglione, David M Mueller, Anurag P Srivastava. Sci Rep 2020
130
13

The Phyre2 web portal for protein modeling, prediction and analysis.
Lawrence A Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J E Sternberg. Nat Protoc 2015
13

AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes.
Neelam Sharma, Sumeet Patiyal, Anjali Dhall, Akshara Pande, Chakit Arora, Gajendra P S Raghava. Brief Bioinform 2021
61
21

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
12

GalaxyWEB server for protein structure prediction and refinement.
Junsu Ko, Hahnbeom Park, Lim Heo, Chaok Seok. Nucleic Acids Res 2012
349
12

Fusion protein linkers: property, design and functionality.
Xiaoying Chen, Jennica L Zaro, Wei-Chiang Shen. Adv Drug Deliv Rev 2013
798
12

UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
12

AlgPred: prediction of allergenic proteins and mapping of IgE epitopes.
Sudipto Saha, G P S Raghava. Nucleic Acids Res 2006
389
12

Computer-aided designing of immunosuppressive peptides based on IL-10 inducing potential.
Gandharva Nagpal, Salman Sadullah Usmani, Sandeep Kumar Dhanda, Harpreet Kaur, Sandeep Singh, Meenu Sharma, Gajendra P S Raghava. Sci Rep 2017
106
12


SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
12


Prediction of residues in discontinuous B-cell epitopes using protein 3D structures.
Pernille Haste Andersen, Morten Nielsen, Ole Lund. Protein Sci 2006
372
12

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

A novel design of a multi-antigenic, multistage and multi-epitope vaccine against Helicobacter pylori: An in silico approach.
Beatriz Meza, Felipe Ascencio, Arturo Pedro Sierra-Beltrán, Javier Torres, Carlos Angulo. Infect Genet Evol 2017
101
11

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Nancy Y Yu, James R Wagner, Matthew R Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S Cenk Sahinalp, Martin Ester, Leonard J Foster,[...]. Bioinformatics 2010
11


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.