A citation-based method for searching scientific literature

Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin. Protein Sci 2018
Times Cited: 1025







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



Times Cited
  Times     Co-cited
Similarity


Distinct conformational states of SARS-CoV-2 spike protein.
Yongfei Cai, Jun Zhang, Tianshu Xiao, Hanqin Peng, Sarah M Sterling, Richard M Walsh, Shaun Rawson, Sophia Rits-Volloch, Bing Chen. Science 2020
303
3

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion.
Alexandra C Walls, Xiaoli Xiong, Young-Jun Park, M Alejandra Tortorici, Joost Snijder, Joel Quispe, Elisabetta Cameroni, Robin Gopal, Mian Dai, Antonio Lanzavecchia,[...]. Cell 2019
303
3

Benchmarking fold detection by DaliLite v.5.
Liisa Holm. Bioinformatics 2019
182
3


Scalable molecular dynamics with NAMD.
James C Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D Skeel, Laxmikant Kalé, Klaus Schulten. J Comput Chem 2005
3

A polymorphic helix of a Salmonella needle protein relays signals defining distinct steps in type III secretion.
Emily Z Guo, Daniel C Desrosiers, Jan Zalesak, James Tolchard, Mélanie Berbon, Birgit Habenstein, Thomas Marlovits, Antoine Loquet, Jorge E Galán. PLoS Biol 2019
13
23

Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin.
J Hu, L J Worrall, C Hong, M Vuckovic, C E Atkinson, N Caveney, Z Yu, N C J Strynadka. Nat Commun 2018
52
5

Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
3

A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2.
Yan Wu, Feiran Wang, Chenguang Shen, Weiyu Peng, Delin Li, Cheng Zhao, Zhaohui Li, Shihua Li, Yuhai Bi, Yang Yang,[...]. Science 2020
485
3


Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody.
Zhe Lv, Yong-Qiang Deng, Qing Ye, Lei Cao, Chun-Yun Sun, Changfa Fan, Weijin Huang, Shihui Sun, Yao Sun, Ling Zhu,[...]. Science 2020
159
3

NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
3

Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants.
Yiska Weisblum, Fabian Schmidt, Fengwen Zhang, Justin DaSilva, Daniel Poston, Julio Cc Lorenzi, Frauke Muecksch, Magdalena Rutkowska, Hans-Heinrich Hoffmann, Eleftherios Michailidis,[...]. Elife 2020
453
3

Structural basis of a shared antibody response to SARS-CoV-2.
Meng Yuan, Hejun Liu, Nicholas C Wu, Chang-Chun D Lee, Xueyong Zhu, Fangzhu Zhao, Deli Huang, Wenli Yu, Yuanzi Hua, Henry Tien,[...]. Science 2020
211
3

Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2.
James Brett Case, Paul W Rothlauf, Rita E Chen, Zhuoming Liu, Haiyan Zhao, Arthur S Kim, Louis-Marie Bloyet, Qiru Zeng, Stephen Tahan, Lindsay Droit,[...]. Cell Host Microbe 2020
145
3

Human monoclonal antibody combination against SARS coronavirus: synergy and coverage of escape mutants.
Jan ter Meulen, Edward N van den Brink, Leo L M Poon, Wilfred E Marissen, Cynthia S W Leung, Freek Cox, Chung Y Cheung, Arjen Q Bakker, Johannes A Bogaards, Els van Deventer,[...]. PLoS Med 2006
360
3

Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.
Tyler N Starr, Allison J Greaney, Sarah K Hilton, Daniel Ellis, Katharine H D Crawford, Adam S Dingens, Mary Jane Navarro, John E Bowen, M Alejandra Tortorici, Alexandra C Walls,[...]. Cell 2020
484
3

Clustal W and Clustal X version 2.0.
M A Larkin, G Blackshields, N P Brown, R Chenna, P A McGettigan, H McWilliam, F Valentin, I M Wallace, A Wilm, R Lopez,[...]. Bioinformatics 2007
3

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
3

Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes.
Serban L Ilca, Abhay Kotecha, Xiaoyu Sun, Minna M Poranen, David I Stuart, Juha T Huiskonen. Nat Commun 2015
123
3

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.
Luca Piccoli, Young-Jun Park, M Alejandra Tortorici, Nadine Czudnochowski, Alexandra C Walls, Martina Beltramello, Chiara Silacci-Fregni, Dora Pinto, Laura E Rosen, John E Bowen,[...]. Cell 2020
309
3

Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability.
Philip J M Brouwer, Tom G Caniels, Karlijn van der Straten, Jonne L Snitselaar, Yoann Aldon, Sandhya Bangaru, Jonathan L Torres, Nisreen M A Okba, Mathieu Claireaux, Gius Kerster,[...]. Science 2020
500
3

Namdinator - automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps.
Rune Thomas Kidmose, Jonathan Juhl, Poul Nissen, Thomas Boesen, Jesper Lykkegaard Karlsen, Bjørn Panyella Pedersen. IUCrJ 2019
65
4

HOLE: a program for the analysis of the pore dimensions of ion channel structural models.
O S Smart, J G Neduvelil, X Wang, B A Wallace, M S Sansom. J Mol Graph 1996
872
3

MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.
Ian W Davis, Laura Weston Murray, Jane S Richardson, David C Richardson. Nucleic Acids Res 2004
751
3

Using Dali for Protein Structure Comparison.
Liisa Holm. Methods Mol Biol 2020
26
11

JPred4: a protein secondary structure prediction server.
Alexey Drozdetskiy, Christian Cole, James Procter, Geoffrey J Barton. Nucleic Acids Res 2015
881
3

Xmipp 3.0: an improved software suite for image processing in electron microscopy.
J M de la Rosa-Trevín, J Otón, R Marabini, A Zaldívar, J Vargas, J M Carazo, C O S Sorzano. J Struct Biol 2013
164
3


Single-particle cryo-EM at atomic resolution.
Takanori Nakane, Abhay Kotecha, Andrija Sente, Greg McMullan, Simonas Masiulis, Patricia M G E Brown, Ioana T Grigoras, Lina Malinauskaite, Tomas Malinauskas, Jonas Miehling,[...]. Nature 2020
137
3

Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine.
Fernando P Polack, Stephen J Thomas, Nicholas Kitchin, Judith Absalon, Alejandra Gurtman, Stephen Lockhart, John L Perez, Gonzalo Pérez Marc, Edson D Moreira, Cristiano Zerbini,[...]. N Engl J Med 2020
3

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Christopher O Barnes, Claudia A Jette, Morgan E Abernathy, Kim-Marie A Dam, Shannon R Esswein, Harry B Gristick, Andrey G Malyutin, Naima G Sharaf, Kathryn E Huey-Tubman, Yu E Lee,[...]. Nature 2020
322
3

An interactive web-based dashboard to track COVID-19 in real time.
Ensheng Dong, Hongru Du, Lauren Gardner. Lancet Infect Dis 2020
3

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.
Leonid Yurkovetskiy, Xue Wang, Kristen E Pascal, Christopher Tomkins-Tinch, Thomas P Nyalile, Yetao Wang, Alina Baum, William E Diehl, Ann Dauphin, Claudia Carbone,[...]. Cell 2020
324
3

The structure of the yeast mitochondrial ribosome.
Nirupa Desai, Alan Brown, Alexey Amunts, V Ramakrishnan. Science 2017
90
2

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
2

Structure and Function of the Mitochondrial Ribosome.
Basil J Greber, Nenad Ban. Annu Rev Biochem 2016
118
2

Structure of the Human Mitochondrial Ribosome Studied In Situ by Cryoelectron Tomography.
Robert Englmeier, Stefan Pfeffer, Friedrich Förster. Structure 2017
39
5

A new system for naming ribosomal proteins.
Nenad Ban, Roland Beckmann, Jamie H D Cate, Jonathan D Dinman, François Dragon, Steven R Ellis, Denis L J Lafontaine, Lasse Lindahl, Anders Liljas, Jeffrey M Lipton,[...]. Curr Opin Struct Biol 2014
315
2

Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.
David J F Ramrath, Moritz Niemann, Marc Leibundgut, Philipp Bieri, Céline Prange, Elke K Horn, Alexander Leitner, Daniel Boehringer, André Schneider, Nenad Ban. Science 2018
53
3

Universal sample preparation method for proteome analysis.
Jacek R Wiśniewski, Alexandre Zougman, Nagarjuna Nagaraj, Matthias Mann. Nat Methods 2009
2


The Pfam protein families database in 2019.
Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R Eddy, Aurélien Luciani, Simon C Potter, Matloob Qureshi, Lorna J Richardson, Gustavo A Salazar, Alfredo Smart,[...]. Nucleic Acids Res 2019
2

High-resolution structure of the Escherichia coli ribosome.
Jonas Noeske, Michael R Wasserman, Daniel S Terry, Roger B Altman, Scott C Blanchard, Jamie H D Cate. Nat Struct Mol Biol 2015
134
2


Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM.
Eva Kummer, Marc Leibundgut, Oliver Rackham, Richard G Lee, Daniel Boehringer, Aleksandra Filipovska, Nenad Ban. Nature 2018
49
4

Cryo-EM structure of the RNA-rich plant mitochondrial ribosome.
Florent Waltz, Heddy Soufari, Anthony Bochler, Philippe Giegé, Yaser Hashem. Nat Plants 2020
20
10

Iron-Sequestering Nanocompartments as Multiplexed Electron Microscopy Gene Reporters.
Felix Sigmund, Susanne Pettinger, Massimo Kube, Fabian Schneider, Martina Schifferer, Steffen Schneider, Maria V Efremova, Jesús Pujol-Martí, Michaela Aichler, Axel Walch,[...]. ACS Nano 2019
14
14


Bacterial encapsulins as orthogonal compartments for mammalian cell engineering.
Felix Sigmund, Christoph Massner, Philipp Erdmann, Anja Stelzl, Hannes Rolbieski, Mitul Desai, Sarah Bricault, Tobias P Wörner, Joost Snijder, Arie Geerlof,[...]. Nat Commun 2018
33
6


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.