A citation-based method for searching scientific literature

Takanori Nakane, Abhay Kotecha, Andrija Sente, Greg McMullan, Simonas Masiulis, Patricia M G E Brown, Ioana T Grigoras, Lina Malinauskaite, Tomas Malinauskas, Jonas Miehling, Tomasz Uchański, Lingbo Yu, Dimple Karia, Evgeniya V Pechnikova, Erwin de Jong, Jeroen Keizer, Maarten Bischoff, Jamie McCormack, Peter Tiemeijer, Steven W Hardwick, Dimitri Y Chirgadze, Garib Murshudov, A Radu Aricescu, Sjors H W Scheres. Nature 2020
Times Cited: 274







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



Times Cited
  Times     Co-cited
Similarity


Atomic-resolution protein structure determination by cryo-EM.
Ka Man Yip, Niels Fischer, Elham Paknia, Ashwin Chari, Holger Stark. Nature 2020
202
60

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
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
24

Biochemistry. The resolution revolution.
Werner Kühlbrandt. Science 2014
601
24

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
22

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
21


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
17


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
16

Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
772
15

Cryo-electron microscopy of vitrified specimens.
J Dubochet, M Adrian, J J Chang, J C Homo, J Lepault, A W McDowall, P Schultz. Q Rev Biophys 1988
15

Resolving individual atoms of protein complex by cryo-electron microscopy.
Kaiming Zhang, Grigore D Pintilie, Shanshan Li, Michael F Schmid, Wah Chiu. Cell Res 2020
31
45

Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells.
Dimitry Tegunov, Liang Xue, Christian Dienemann, Patrick Cramer, Julia Mahamid. Nat Methods 2021
87
16

CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
14


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
13



CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks.
Ellen D Zhong, Tristan Bepler, Bonnie Berger, Joseph H Davis. Nat Methods 2021
91
13

Cryo-EM with sub-1 Å specimen movement.
Katerina Naydenova, Peipei Jia, Christopher J Russo. Science 2020
45
24

Real-time cryo-electron microscopy data preprocessing with Warp.
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
329
11

Structure of the TRPV1 ion channel determined by electron cryo-microscopy.
Maofu Liao, Erhu Cao, David Julius, Yifan Cheng. Nature 2013
11

A primer to single-particle cryo-electron microscopy.
Yifan Cheng, Nikolaus Grigorieff, Pawel A Penczek, Thomas Walz. Cell 2015
292
10

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
10


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
10

Quantifying the local resolution of cryo-EM density maps.
Alp Kucukelbir, Fred J Sigworth, Hemant D Tagare. Nat Methods 2014
10

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
10

How cryo-EM is revolutionizing structural biology.
Xiao-chen Bai, Greg McMullan, Sjors H W Scheres. Trends Biochem Sci 2015
435
10


Time-resolved cryo-EM using Spotiton.
Venkata P Dandey, William C Budell, Hui Wei, Daija Bobe, Kashyap Maruthi, Mykhailo Kopylov, Edward T Eng, Peter A Kahn, Jenny E Hinshaw, Nidhi Kundu,[...]. Nat Methods 2020
46
19

CryoEM at 100 keV: a demonstration and prospects.
K Naydenova, G McMullan, M J Peet, Y Lee, P C Edwards, S Chen, E Leahy, S Scotcher, R Henderson, C J Russo. IUCrJ 2019
48
18

Specimen Preparation for High-Resolution Cryo-EM.
L A Passmore, C J Russo. Methods Enzymol 2016
80
11




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
9

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
9

Recent developments in the CCP-EM software suite.
Tom Burnley, Colin M Palmer, Martyn Winn. Acta Crystallogr D Struct Biol 2017
156
9



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
8

Cryo-EM structures from sub-nl volumes using pin-printing and jet vitrification.
Raimond B G Ravelli, Frank J T Nijpels, Rene J M Henderikx, Giulia Weissenberger, Sanne Thewessem, Abril Gijsbers, Bart W A M M Beulen, Carmen López-Iglesias, Peter J Peters. Nat Commun 2020
52
15

Protein denaturation at the air-water interface and how to prevent it.
Edoardo D'Imprima, Davide Floris, Mirko Joppe, Ricardo Sánchez, Martin Grininger, Werner Kühlbrandt. Elife 2019
115
8

Highly accurate protein structure prediction for the human proteome.
Kathryn Tunyasuvunakool, Jonas Adler, Zachary Wu, Tim Green, Michal Zielinski, Augustin Žídek, Alex Bridgland, Andrew Cowie, Clemens Meyer, Agata Laydon,[...]. Nature 2021
554
8

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.
Florian K M Schur, Martin Obr, Wim J H Hagen, William Wan, Arjen J Jakobi, Joanna M Kirkpatrick, Carsten Sachse, Hans-Georg Kräusslich, John A G Briggs. Science 2016
238
8

High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy.
Yimo Han, Xiao Fan, Haozhe Wang, Fang Zhao, Christopher G Tully, Jing Kong, Nan Yao, Nieng Yan. Proc Natl Acad Sci U S A 2020
39
20


Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution.
Xiao Fan, Jia Wang, Xing Zhang, Zi Yang, Jin-Can Zhang, Lingyun Zhao, Hai-Lin Peng, Jianlin Lei, Hong-Wei Wang. Nat Commun 2019
66
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.