A citation-based method for searching scientific literature

Guang Tang, Liwei Peng, Philip R Baldwin, Deepinder S Mann, Wen Jiang, Ian Rees, Steven J Ludtke. J Struct Biol 2007
Times Cited: 1874







List of co-cited articles
450 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
56

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
43


CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
38

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
32

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
29

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
25


cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
23

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
22


cisTEM, user-friendly software for single-particle image processing.
Timothy Grant, Alexis Rohou, Nikolaus Grigorieff. Elife 2018
335
17

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
996
15

Computer visualization of three-dimensional image data using IMOD.
J R Kremer, D N Mastronarde, J R McIntosh. J Struct Biol 1996
13

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
12


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

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
10

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
571
9


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
891
8

NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
7

Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.
Dari Kimanius, Björn O Forsberg, Sjors Hw Scheres, Erik Lindahl. Elife 2016
608
7

Accurate determination of local defocus and specimen tilt in electron microscopy.
Joseph A Mindell, Nikolaus Grigorieff. J Struct Biol 2003
7

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
214
7




Beam-induced motion of vitrified specimen on holey carbon film.
Axel F Brilot, James Z Chen, Anchi Cheng, Junhua Pan, Stephen C Harrison, Clinton S Potter, Bridget Carragher, Richard Henderson, Nikolaus Grigorieff. J Struct Biol 2012
224
6

Real-time cryo-electron microscopy data preprocessing with Warp.
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
185
6

Convolutional neural networks for automated annotation of cellular cryo-electron tomograms.
Muyuan Chen, Wei Dai, Stella Y Sun, Darius Jonasch, Cynthia Y He, Michael F Schmid, Wah Chiu, Steven J Ludtke. Nat Methods 2017
101
6

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
6

XDS.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
6

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
972
6

Automated tilt series alignment and tomographic reconstruction in IMOD.
David N Mastronarde, Susannah R Held. J Struct Biol 2017
150
6

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
6

Structures and distributions of SARS-CoV-2 spike proteins on intact virions.
Zunlong Ke, Joaquin Oton, Kun Qu, Mirko Cortese, Vojtech Zila, Lesley McKeane, Takanori Nakane, Jasenko Zivanov, Christopher J Neufeldt, Berati Cerikan,[...]. Nature 2020
252
6

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
63
9

SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields.
J Frank, M Radermacher, P Penczek, J Zhu, Y Li, M Ladjadj, A Leith. J Struct Biol 1996
5

Focused-ion-beam thinning of frozen-hydrated biological specimens for cryo-electron microscopy.
Michael Marko, Chyongere Hsieh, Richard Schalek, Joachim Frank, Carmen Mannella. Nat Methods 2007
241
5

Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å.
Beata Turoňová, Florian K M Schur, William Wan, John A G Briggs. J Struct Biol 2017
84
5


Visualizing density maps with UCSF Chimera.
Thomas D Goddard, Conrad C Huang, Thomas E Ferrin. J Struct Biol 2007
526
5


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
247
5


Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography.
Alexander Rigort, Felix J B Bäuerlein, Elizabeth Villa, Matthias Eibauer, Tim Laugks, Wolfgang Baumeister, Jürgen M Plitzko. Proc Natl Acad Sci U S A 2012
188
5

Helical reconstruction in RELION.
Shaoda He, Sjors H W Scheres. J Struct Biol 2017
162
5

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
381
5

Rapid tilt-series acquisition for electron cryotomography.
Georges Chreifi, Songye Chen, Lauren Ann Metskas, Mohammed Kaplan, Grant J Jensen. J Struct Biol 2019
34
11


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.