A citation-based method for searching scientific literature

Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
Times Cited: 2828







List of co-cited articles
209 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
14


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
11

Improved protein structure prediction using predicted interresidue orientations.
Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2020
284
8

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
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
909
7


Improved protein structure prediction using potentials from deep learning.
Andrew W Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W R Nelson, Alex Bridgland,[...]. Nature 2020
524
6

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
6

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
5

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
5

Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
5



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
868
5

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
5


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
5

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
5



MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
5


GalaxyRefine: Protein structure refinement driven by side-chain repacking.
Lim Heo, Hahnbeom Park, Chaok Seok. Nucleic Acids Res 2013
283
4


Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.
Daniel Wrapp, Nianshuang Wang, Kizzmekia S Corbett, Jory A Goldsmith, Ching-Lin Hsieh, Olubukola Abiona, Barney S Graham, Jason S McLellan. Science 2020
4

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.
Hetunandan Kamisetty, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2013
355
4

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
4

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
4

Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13).
Andrew W Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W R Nelson, Alex Bridgland,[...]. Proteins 2019
93
4

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
Stéphane Guindon, Jean-François Dufayard, Vincent Lefort, Maria Anisimova, Wim Hordijk, Olivier Gascuel. Syst Biol 2010
4

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments.
David T Jones, Daniel W A Buchan, Domenico Cozzetto, Massimiliano Pontil. Bioinformatics 2012
431
4




Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu. PLoS Comput Biol 2017
346
4




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
765
3

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
3

The proximal origin of SARS-CoV-2.
Kristian G Andersen, Andrew Rambaut, W Ian Lipkin, Edward C Holmes, Robert F Garry. Nat Med 2020
3

Site-specific glycan analysis of the SARS-CoV-2 spike.
Yasunori Watanabe, Joel D Allen, Daniel Wrapp, Jason S McLellan, Max Crispin. Science 2020
574
3


CHARMM: the biomolecular simulation program.
B R Brooks, C L Brooks, A D Mackerell, L Nilsson, R J Petrella, B Roux, Y Won, G Archontis, C Bartels, S Boresch,[...]. J Comput Chem 2009
3

Protein structure prediction and analysis using the Robetta server.
David E Kim, Dylan Chivian, David Baker. Nucleic Acids Res 2004
3


Protein homology detection by HMM-HMM comparison.
Johannes Söding. Bioinformatics 2005
3


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.