A citation-based method for searching scientific literature

Markus Wiederstein, Manfred J Sippl. Nucleic Acids Res 2007
Times Cited: 2414







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



Times Cited
  Times     Co-cited
Similarity



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
23


VERIFY3D: assessment of protein models with three-dimensional profiles.
D Eisenberg, R Lüthy, J U Bowie. Methods Enzymol 1997
18

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
461
16

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
726
15


Designing of interferon-gamma inducing MHC class-II binders.
Sandeep Kumar Dhanda, Pooja Vir, Gajendra P S Raghava. Biol Direct 2013
175
14

GalaxyRefine: Protein structure refinement driven by side-chain repacking.
Lim Heo, Hahnbeom Park, Chaok Seok. Nucleic Acids Res 2013
262
13

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
456
13

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
12

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.
Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
12

AllerTOP v.2--a server for in silico prediction of allergens.
Ivan Dimitrov, Ivan Bangov, Darren R Flower, Irini Doytchinova. J Mol Model 2014
155
12

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
310
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
11

Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
Simon C Lovell, Ian W Davis, W Bryan Arendall, Paul I W de Bakker, J Michael Word, Michael G Prisant, Jane S Richardson, David C Richardson. Proteins 2003
11


Comparative Protein Structure Modeling Using MODELLER.
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
910
10

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
125
10

PatchDock and SymmDock: servers for rigid and symmetric docking.
Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J Wolfson. Nucleic Acids Res 2005
10

GalaxyWEB server for protein structure prediction and refinement.
Junsu Ko, Hahnbeom Park, Lim Heo, Chaok Seok. Nucleic Acids Res 2012
220
10

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
82
12

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
10

Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection.
Mudassar Ali, Rajan Kumar Pandey, Nazia Khatoon, Aruna Narula, Amit Mishra, Vijay Kumar Prajapati. Sci Rep 2017
101
10


VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
9

AlgPred: prediction of allergenic proteins and mapping of IgE epitopes.
Sudipto Saha, G P S Raghava. Nucleic Acids Res 2006
317
9

A new coronavirus associated with human respiratory disease in China.
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Zhi-Gang Song, Yi Hu, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei,[...]. Nature 2020
9


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
357
9




PDBsum: Structural summaries of PDB entries.
Roman A Laskowski, Jagoda Jabłońska, Lukáš Pravda, Radka Svobodová Vařeková, Janet M Thornton. Protein Sci 2018
259
8

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
8

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
8

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
8

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
264
8

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
8


AllergenFP: allergenicity prediction by descriptor fingerprints.
Ivan Dimitrov, Lyudmila Naneva, Irini Doytchinova, Ivan Bangov. Bioinformatics 2014
145
8


Design of the linkers which effectively separate domains of a bifunctional fusion protein.
R Arai, H Ueda, A Kitayama, N Kamiya, T Nagamune. Protein Eng 2001
324
8

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
8

Toward the estimation of the absolute quality of individual protein structure models.
Pascal Benkert, Marco Biasini, Torsten Schwede. Bioinformatics 2011
7

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.
G C P van Zundert, J P G L M Rodrigues, M Trellet, C Schmitz, P L Kastritis, E Karaca, A S J Melquiond, M van Dijk, S J de Vries, A M J J Bonvin. J Mol Biol 2016
826
7

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R Shirts, Jeremy C Smith, Peter M Kasson, David van der Spoel,[...]. Bioinformatics 2013
7

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
7

Assessment of protein models with three-dimensional profiles.
R Lüthy, J U Bowie, D Eisenberg. Nature 1992
7

Template-based protein structure modeling using the RaptorX web server.
Morten Källberg, Haipeng Wang, Sheng Wang, Jian Peng, Zhiyong Wang, Hui Lu, Jinbo Xu. Nat Protoc 2012
871
7


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.