A citation-based method for searching scientific literature

Christian Suloway, James Pulokas, Denis Fellmann, Anchi Cheng, Francisco Guerra, Joel Quispe, Scott Stagg, Clinton S Potter, Bridget Carragher. J Struct Biol 2005
Times Cited: 1096







List of co-cited articles
737 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
69

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
64

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
49

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
41

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
39

CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
31

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
29


Appion: an integrated, database-driven pipeline to facilitate EM image processing.
Gabriel C Lander, Scott M Stagg, Neil R Voss, Anchi Cheng, Denis Fellmann, James Pulokas, Craig Yoshioka, Christopher Irving, Anke Mulder, Pick-Wei Lau,[...]. J Struct Biol 2009
603
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
27

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
23

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
23

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
22

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
21

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
20

DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy.
N R Voss, C K Yoshioka, M Radermacher, C S Potter, B Carragher. J Struct Biol 2009
418
20

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
19

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.
Ray Yu-Ruei Wang, Yifan Song, Benjamin A Barad, Yifan Cheng, James S Fraser, Frank DiMaio. Elife 2016
227
18


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
17

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

Addressing preferred specimen orientation in single-particle cryo-EM through tilting.
Yong Zi Tan, Philip R Baldwin, Joseph H Davis, James R Williamson, Clinton S Potter, Bridget Carragher, Dmitry Lyumkis. Nat Methods 2017
365
15

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
14


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
14

Real-time cryo-electron microscopy data preprocessing with Warp.
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
329
13

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
12


Inference of macromolecular assemblies from crystalline state.
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
11

Broad sarbecovirus neutralization by a human monoclonal antibody.
M Alejandra Tortorici, Nadine Czudnochowski, Tyler N Starr, Roberta Marzi, Alexandra C Walls, Fabrizia Zatta, John E Bowen, Stefano Jaconi, Julia Di Iulio, Zhaoqian Wang,[...]. Nature 2021
113
11

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
11

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
10

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
722
10

cisTEM, user-friendly software for single-particle image processing.
Timothy Grant, Alexis Rohou, Nikolaus Grigorieff. Elife 2018
453
9

Broad betacoronavirus neutralization by a stem helix-specific human antibody.
Dora Pinto, Maximilian M Sauer, Nadine Czudnochowski, Jun Siong Low, M Alejandra Tortorici, Michael P Housley, Julia Noack, Alexandra C Walls, John E Bowen, Barbara Guarino,[...]. Science 2021
112
9

Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen.
Jesper Pallesen, Nianshuang Wang, Kizzmekia S Corbett, Daniel Wrapp, Robert N Kirchdoerfer, Hannah L Turner, Christopher A Cottrell, Michelle M Becker, Lingshu Wang, Wei Shi,[...]. Proc Natl Acad Sci U S A 2017
612
9

mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection.
Leonidas Stamatatos, Julie Czartoski, Yu-Hsin Wan, Leah J Homad, Vanessa Rubin, Hayley Glantz, Moni Neradilek, Emilie Seydoux, Madeleine F Jennewein, Anna J MacCamy,[...]. Science 2021
298
9

SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape.
Tyler N Starr, Nadine Czudnochowski, Zhuoming Liu, Fabrizia Zatta, Young-Jun Park, Amin Addetia, Dora Pinto, Martina Beltramello, Patrick Hernandez, Allison J Greaney,[...]. Nature 2021
172
9

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
9

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
9

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2.
Matthew McCallum, Anna De Marco, Florian A Lempp, M Alejandra Tortorici, Dora Pinto, Alexandra C Walls, Martina Beltramello, Alex Chen, Zhuoming Liu, Fabrizia Zatta,[...]. Cell 2021
440
9

Commonality despite exceptional diversity in the baseline human antibody repertoire.
Bryan Briney, Anne Inderbitzin, Collin Joyce, Dennis R Burton. Nature 2019
216
9

Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike.
Lihong Liu, Pengfei Wang, Manoj S Nair, Jian Yu, Micah Rapp, Qian Wang, Yang Luo, Jasper F-W Chan, Vincent Sahi, Amir Figueroa,[...]. Nature 2020
866
8

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
8

Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity.
Hejun Liu, Nicholas C Wu, Meng Yuan, Sandhya Bangaru, Jonathan L Torres, Tom G Caniels, Jelle van Schooten, Xueyong Zhu, Chang-Chun D Lee, Philip J M Brouwer,[...]. Immunity 2020
123
8

Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies.
Claudia A Jette, Alexander A Cohen, Priyanthi N P Gnanapragasam, Frauke Muecksch, Yu E Lee, Kathryn E Huey-Tubman, Fabian Schmidt, Theodora Hatziioannou, Paul D Bieniasz, Michel C Nussenzweig,[...]. Cell Rep 2021
40
20

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
8

EMAN2: an extensible image processing suite for electron microscopy.
Guang Tang, Liwei Peng, Philip R Baldwin, Deepinder S Mann, Wen Jiang, Ian Rees, Steven J Ludtke. J Struct Biol 2007
8

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
8


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.