A citation-based method for searching scientific literature

Rangana Warshamanage, Keitaro Yamashita, Garib N Murshudov. J Struct Biol 2022
Times Cited: 8







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



Times Cited
  Times     Co-cited
Similarity



cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
50

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
50


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
37

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
37

Atomic-resolution protein structure determination by cryo-EM.
Ka Man Yip, Niels Fischer, Elham Paknia, Ashwin Chari, Holger Stark. Nature 2020
202
37

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
37

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.
Catherine L Lawson, Andriy Kryshtafovych, Paul D Adams, Pavel V Afonine, Matthew L Baker, Benjamin A Barad, Paul Bond, Tom Burnley, Renzhi Cao, Jianlin Cheng,[...]. Nat Methods 2021
31
37

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
274
37

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
37

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
37

Structural Characterization of N-Linked Glycans in the Receptor Binding Domain of the SARS-CoV-2 Spike Protein and their Interactions with Human Lectins.
Maria Pia Lenza, Iker Oyenarte, Tammo Diercks, Jon Imanol Quintana, Ana Gimeno, Helena Coelho, Ana Diniz, Francesca Peccati, Sandra Delgado, Alexandre Bosch,[...]. Angew Chem Int Ed Engl 2020
51
25

CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
25

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
25

Site-specific glycan analysis of the SARS-CoV-2 spike.
Yasunori Watanabe, Joel D Allen, Daniel Wrapp, Jason S McLellan, Max Crispin. Science 2020
812
25

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein.
Lorenzo Casalino, Zied Gaieb, Jory A Goldsmith, Christy K Hjorth, Abigail C Dommer, Aoife M Harbison, Carl A Fogarty, Emilia P Barros, Bryn C Taylor, Jason S McLellan,[...]. ACS Cent Sci 2020
400
25

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
25

SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM.
Thorsten Wagner, Felipe Merino, Markus Stabrin, Toshio Moriya, Claudia Antoni, Amir Apelbaum, Philine Hagel, Oleg Sitsel, Tobias Raisch, Daniel Prumbaum,[...]. Commun Biol 2019
402
25

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.
Ingvar Lagerstedt, William J Moore, Ardan Patwardhan, Eduardo Sanz-García, Christoph Best, Jason R Swedlow, Gerard J Kleywegt. J Struct Biol 2013
21
25

REFMAC5 for the refinement of macromolecular crystal structures.
Garib N Murshudov, Pavol Skubák, Andrey A Lebedev, Navraj S Pannu, Roberto A Steiner, Robert A Nicholls, Martyn D Winn, Fei Long, Alexei A Vagin. Acta Crystallogr D Biol Crystallogr 2011
25

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
25

Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein.
Christine Toelzer, Kapil Gupta, Sathish K N Yadav, Ufuk Borucu, Andrew D Davidson, Maia Kavanagh Williamson, Deborah K Shoemark, Frederic Garzoni, Oskar Staufer, Rachel Milligan,[...]. Science 2020
200
25


Measurement of atom resolvability in cryo-EM maps with Q-scores.
Grigore Pintilie, Kaiming Zhang, Zhaoming Su, Shanshan Li, Michael F Schmid, Wah Chiu. Nat Methods 2020
80
25

One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions.
Giovanni Cardone, J Bernard Heymann, Alasdair C Steven. J Struct Biol 2013
215
25

Errors in protein structures.
R W Hooft, G Vriend, C Sander, E E Abola. Nature 1996
25

Biochemistry. The resolution revolution.
Werner Kühlbrandt. Science 2014
601
25

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
25

Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment.
Agnel Praveen Joseph, Sony Malhotra, Tom Burnley, Chris Wood, Daniel K Clare, Martyn Winn, Maya Topf. Methods 2016
64
25

Recent developments in the CCP-EM software suite.
Tom Burnley, Colin M Palmer, Martyn Winn. Acta Crystallogr D Struct Biol 2017
156
25

Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM.
Robert A Nicholls, Michal Tykac, Oleg Kovalevskiy, Garib N Murshudov. Acta Crystallogr D Struct Biol 2018
53
25


Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.
Agnel Praveen Joseph, Ingvar Lagerstedt, Ardan Patwardhan, Maya Topf, Martyn Winn. J Struct Biol 2017
28
25

Outcome of the first electron microscopy validation task force meeting.
Richard Henderson, Andrej Sali, Matthew L Baker, Bridget Carragher, Batsal Devkota, Kenneth H Downing, Edward H Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff,[...]. Structure 2012
313
25

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
25

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions.
Alan Brown, Fei Long, Robert A Nicholls, Jaan Toots, Paul Emsley, Garib Murshudov. Acta Crystallogr D Biol Crystallogr 2015
366
25

Fitting atomic models into electron-microscopy maps.
M G Rossmann. Acta Crystallogr D Biol Crystallogr 2000
160
25

Assessment of protein-protein interfaces in cryo-EM derived assemblies.
Sony Malhotra, Agnel Praveen Joseph, Jeyan Thiyagalingam, Maya Topf. Nat Commun 2021
7
28

New tools for the analysis and validation of cryo-EM maps and atomic models.
Pavel V Afonine, Bruno P Klaholz, Nigel W Moriarty, Billy K Poon, Oleg V Sobolev, Thomas C Terwilliger, Paul D Adams, Alexandre Urzhumtsev. Acta Crystallogr D Struct Biol 2018
305
25

Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps.
Agnel Praveen Joseph, Ingvar Lagerstedt, Arjen Jakobi, Tom Burnley, Ardan Patwardhan, Maya Topf, Martyn Winn. J Chem Inf Model 2020
15
25


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
25

Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Tongqing Zhou, Yaroslav Tsybovsky, Jason Gorman, Micah Rapp, Gabriele Cerutti, Gwo-Yu Chuang, Phinikoula S Katsamba, Jared M Sampson, Arne Schön, Jude Bimela,[...]. Cell Host Microbe 2020
171
12

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
12

Computational epitope map of SARS-CoV-2 spike protein.
Mateusz Sikora, Sören von Bülow, Florian E C Blanc, Michael Gecht, Roberto Covino, Gerhard Hummer. PLoS Comput Biol 2021
45
12

Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane.
Hyeonuk Woo, Sang-Jun Park, Yeol Kyo Choi, Taeyong Park, Maham Tanveer, Yiwei Cao, Nathan R Kern, Jumin Lee, Min Sun Yeom, Tristan I Croll,[...]. J Phys Chem B 2020
150
12


Identifying the origin of local flexibility in a carbohydrate polymer.
Kelvin Anggara, Yuntao Zhu, Giulio Fittolani, Yang Yu, Theodore Tyrikos-Ergas, Martina Delbianco, Stephan Rauschenbach, Sabine Abb, Peter H Seeberger, Klaus Kern. Proc Natl Acad Sci U S A 2021
5
20

Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies.
Florian A Lempp, Leah B Soriaga, Martin Montiel-Ruiz, Fabio Benigni, Julia Noack, Young-Jun Park, Siro Bianchi, Alexandra C Walls, John E Bowen, Jiayi Zhou,[...]. Nature 2021
117
12


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.