A citation-based method for searching scientific literature

Jasenko Zivanov, Takanori Nakane, Sjors H W Scheres. IUCrJ 2019
Times Cited: 336







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



Times Cited
  Times     Co-cited
Similarity


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
73

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
63

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
55

CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
52

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
52

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
51

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


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
31

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
28



Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
26


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
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
24



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
21

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
20

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
20

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
20


Real-time cryo-electron microscopy data preprocessing with Warp.
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
329
16

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
14


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
14

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
14

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs.
Tristan Bepler, Andrew Morin, Micah Rapp, Julia Brasch, Lawrence Shapiro, Alex J Noble, Bonnie Berger. Nat Methods 2019
210
13

Improvement of cryo-EM maps by density modification.
Thomas C Terwilliger, Steven J Ludtke, Randy J Read, Paul D Adams, Pavel V Afonine. Nat Methods 2020
127
12

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing.
Ruben Sanchez-Garcia, Josue Gomez-Blanco, Ana Cuervo, Jose Maria Carazo, Carlos Oscar S Sorzano, Javier Vargas. Commun Biol 2021
167
12

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
12


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
11

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
11

Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.
Xueming Li, Paul Mooney, Shawn Zheng, Christopher R Booth, Michael B Braunfeld, Sander Gubbens, David A Agard, Yifan Cheng. Nat Methods 2013
11


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
10

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
10

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION.
Takanori Nakane, Dari Kimanius, Erik Lindahl, Sjors Hw Scheres. Elife 2018
246
10

Screening and large-scale expression of membrane proteins in mammalian cells for structural studies.
April Goehring, Chia-Hsueh Lee, Kevin H Wang, Jennifer Carlisle Michel, Derek P Claxton, Isabelle Baconguis, Thorsten Althoff, Suzanne Fischer, K Christopher Garcia, Eric Gouaux. Nat Protoc 2014
325
9

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
9

Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER.
Kailash Ramlaul, Colin M Palmer, Takanori Nakane, Christopher H S Aylett. J Struct Biol 2020
42
21

Atomic-resolution protein structure determination by cryo-EM.
Ka Man Yip, Niels Fischer, Elham Paknia, Ashwin Chari, Holger Stark. Nature 2020
202
8

Amyloid structure determination in RELION-3.1.
Sjors H W Scheres. Acta Crystallogr D Struct Biol 2020
61
13

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
8

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
8


Cryo-EM with sub-1 Å specimen movement.
Katerina Naydenova, Peipei Jia, Christopher J Russo. Science 2020
45
15

Cryo-EM single-particle structure refinement and map calculation using Servalcat.
Keitaro Yamashita, Colin M Palmer, Tom Burnley, Garib N Murshudov. Acta Crystallogr D Struct Biol 2021
23
30


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.