A citation-based method for searching scientific literature

Ray Yu-Ruei Wang, Yifan Song, Benjamin A Barad, Yifan Cheng, James S Fraser, Frank DiMaio. Elife 2016
Times Cited: 227







List of co-cited articles
895 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
70

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
57

New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Jasenko Zivanov, Takanori Nakane, Björn O Forsberg, Dari Kimanius, Wim Jh Hagen, Erik Lindahl, Sjors Hw Scheres. Elife 2018
57

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
53

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy.
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng, David A Agard. Nat Methods 2017
48

MolProbity: all-atom structure validation for macromolecular crystallography.
Vincent B Chen, W Bryan Arendall, Jeffrey J Headd, Daniel A Keedy, Robert M Immormino, Gary J Kapral, Laura W Murray, Jane S Richardson, David C Richardson. Acta Crystallogr D Biol Crystallogr 2010
36

Automated molecular microscopy: the new Leginon system.
Christian Suloway, James Pulokas, Denis Fellmann, Anchi Cheng, Francisco Guerra, Joel Quispe, Scott Stagg, Clinton S Potter, Bridget Carragher. J Struct Biol 2005
36

A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis.
Jasenko Zivanov, Takanori Nakane, Sjors H W Scheres. IUCrJ 2019
336
32

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Paul D Adams, Pavel V Afonine, Gábor Bunkóczi, Vincent B Chen, Ian W Davis, Nathaniel Echols, Jeffrey J Headd, Li-Wei Hung, Gary J Kapral, Ralf W Grosse-Kunstleve,[...]. Acta Crystallogr D Biol Crystallogr 2010
32

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Dorothee Liebschner, Pavel V Afonine, Matthew L Baker, Gábor Bunkóczi, Vincent B Chen, Tristan I Croll, Bradley Hintze, Li Wei Hung, Swati Jain, Airlie J McCoy,[...]. Acta Crystallogr D Struct Biol 2019
29

UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin. Protein Sci 2018
28




UCSF ChimeraX: Structure visualization for researchers, educators, and developers.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Elaine C Meng, Gregory S Couch, Tristan I Croll, John H Morris, Thomas E Ferrin. Protein Sci 2021
25

EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.
Benjamin A Barad, Nathaniel Echols, Ray Yu-Ruei Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James S Fraser. Nat Methods 2015
486
24

Real-time cryo-electron microscopy data preprocessing with Warp.
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
329
24


CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
23

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.
Alexandra C Walls, Young-Jun Park, M Alejandra Tortorici, Abigail Wall, Andrew T McGuire, David Veesler. Cell 2020
22

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
21


Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody.
Dora Pinto, Young-Jun Park, Martina Beltramello, Alexandra C Walls, M Alejandra Tortorici, Siro Bianchi, Stefano Jaconi, Katja Culap, Fabrizia Zatta, Anna De Marco,[...]. Nature 2020
21

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.
Shaoxia Chen, Greg McMullan, Abdul R Faruqi, Garib N Murshudov, Judith M Short, Sjors H W Scheres, Richard Henderson. Ultramicroscopy 2013
554
19

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
665
19

Automatically Fixing Errors in Glycoprotein Structures with Rosetta.
Brandon Frenz, Sebastian Rämisch, Andrew J Borst, Alexandra C Walls, Jared Adolf-Bryfogle, William R Schief, David Veesler, Frank DiMaio. Structure 2019
56
33

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.
M Alejandra Tortorici, Martina Beltramello, Florian A Lempp, Dora Pinto, Ha V Dang, Laura E Rosen, Matthew McCallum, John Bowen, Andrea Minola, Stefano Jaconi,[...]. Science 2020
334
18

MolProbity: More and better reference data for improved all-atom structure validation.
Christopher J Williams, Jeffrey J Headd, Nigel W Moriarty, Michael G Prisant, Lizbeth L Videau, Lindsay N Deis, Vishal Verma, Daniel A Keedy, Bradley J Hintze, Vincent B Chen,[...]. Protein Sci 2018
16


Structure-based design of prefusion-stabilized SARS-CoV-2 spikes.
Ching-Lin Hsieh, Jory A Goldsmith, Jeffrey M Schaub, Andrea M DiVenere, Hung-Che Kuo, Kamyab Javanmardi, Kevin C Le, Daniel Wrapp, Alison G Lee, Yutong Liu,[...]. Science 2020
513
16

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
376
15

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
15

Privateer: software for the conformational validation of carbohydrate structures.
Jon Agirre, Javier Iglesias-Fernández, Carme Rovira, Gideon J Davies, Keith S Wilson, Kevin D Cowtan. Nat Struct Mol Biol 2015
217
15

Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail.
Johanna Hansen, Alina Baum, Kristen E Pascal, Vincenzo Russo, Stephanie Giordano, Elzbieta Wloga, Benjamin O Fulton, Ying Yan, Katrina Koon, Krunal Patel,[...]. Science 2020
743
14

Phaser crystallographic software.
Airlie J McCoy, Ralf W Grosse-Kunstleve, Paul D Adams, Martyn D Winn, Laurent C Storoni, Randy J Read. J Appl Crystallogr 2007
14

Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays.
Katharine H D Crawford, Rachel Eguia, Adam S Dingens, Andrea N Loes, Keara D Malone, Caitlin R Wolf, Helen Y Chu, M Alejandra Tortorici, David Veesler, Michael Murphy,[...]. Viruses 2020
416
14

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
959
14

Real-space refinement in PHENIX for cryo-EM and crystallography.
Pavel V Afonine, Billy K Poon, Randy J Read, Oleg V Sobolev, Thomas C Terwilliger, Alexandre Urzhumtsev, Paul D Adams. Acta Crystallogr D Struct Biol 2018
924
13

Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2.
Alexandra C Walls, Brooke Fiala, Alexandra Schäfer, Samuel Wrenn, Minh N Pham, Michael Murphy, Longping V Tse, Laila Shehata, Megan A O'Connor, Chengbo Chen,[...]. Cell 2020
234
13

Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
13

Broad neutralization of SARS-related viruses by human monoclonal antibodies.
Anna Z Wec, Daniel Wrapp, Andrew S Herbert, Daniel P Maurer, Denise Haslwanter, Mrunal Sakharkar, Rohit K Jangra, M Eugenia Dieterle, Asparouh Lilov, Deli Huang,[...]. Science 2020
380
12

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
257
12

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19.
Tyler N Starr, Allison J Greaney, Amin Addetia, William W Hannon, Manish C Choudhary, Adam S Dingens, Jonathan Z Li, Jesse D Bloom. Science 2021
426
12

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.
Dami A Collier, Anna De Marco, Isabella A T M Ferreira, Bo Meng, Rawlings P Datir, Alexandra C Walls, Steven A Kemp, Jessica Bassi, Dora Pinto, Chiara Silacci-Fregni,[...]. Nature 2021
446
12

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.
Markus Hoffmann, Hannah Kleine-Weber, Simon Schroeder, Nadine Krüger, Tanja Herrler, Sandra Erichsen, Tobias S Schiergens, Georg Herrler, Nai-Huei Wu, Andreas Nitsche,[...]. Cell 2020
12

Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody.
C Garrett Rappazzo, Longping V Tse, Chengzi I Kaku, Daniel Wrapp, Mrunal Sakharkar, Deli Huang, Laura M Deveau, Thomas J Yockachonis, Andrew S Herbert, Michael B Battles,[...]. Science 2021
162
12

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
725
12

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity.
Emma C Thomson, Laura E Rosen, James G Shepherd, Roberto Spreafico, Ana da Silva Filipe, Jason A Wojcechowskyj, Chris Davis, Luca Piccoli, David J Pascall, Josh Dillen,[...]. Cell 2021
358
12

XDS.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
11

Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines.
Alexandra C Walls, Marcos C Miranda, Alexandra Schäfer, Minh N Pham, Allison Greaney, Prabhu S Arunachalam, Mary-Jane Navarro, M Alejandra Tortorici, Kenneth Rogers, Megan A O'Connor,[...]. Cell 2021
66
16


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.