A citation-based method for searching scientific literature

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
Times Cited: 269







List of co-cited articles
537 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
67

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
61

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
52

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
809
46

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
39

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
35



Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
28

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
28

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
27

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
26


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

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

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
24

Quantifying the local resolution of cryo-EM density maps.
Alp Kucukelbir, Fred J Sigworth, Hemant D Tagare. Nat Methods 2014
22



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
459
12

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
12

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
723
12

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
11

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
325
11

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
338
11

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
11

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
63
15

A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis.
Jasenko Zivanov, Takanori Nakane, Sjors H W Scheres. IUCrJ 2019
287
10

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
113
10

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
9

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
356
9

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
530
9


cisTEM, user-friendly software for single-particle image processing.
Timothy Grant, Alexis Rohou, Nikolaus Grigorieff. Elife 2018
416
9

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.
J M de la Rosa-Trevín, A Quintana, L Del Cano, A Zaldívar, I Foche, J Gutiérrez, J Gómez-Blanco, J Burguet-Castell, J Cuenca-Alba, V Abrishami,[...]. J Struct Biol 2016
260
9

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
202
8

Prevention of overfitting in cryo-EM structure determination.
Sjors H W Scheres, Shaoxia Chen. Nat Methods 2012
746
8

Automated map sharpening by maximization of detail and connectivity.
Thomas C Terwilliger, Oleg V Sobolev, Pavel V Afonine, Paul D Adams. Acta Crystallogr D Struct Biol 2018
106
8

Real-time cryo-electron microscopy data preprocessing with Warp.
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
283
8

Inference of macromolecular assemblies from crystalline state.
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
8

Recent developments in the CCP-EM software suite.
Tom Burnley, Colin M Palmer, Martyn Winn. Acta Crystallogr D Struct Biol 2017
140
8

Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
8


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
47
14

TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits.
Irene Farabella, Daven Vasishtan, Agnel Praveen Joseph, Arun Prasad Pandurangan, Harpal Sahota, Maya Topf. J Appl Crystallogr 2015
49
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
7

Software tools for automated transmission electron microscopy.
Martin Schorb, Isabella Haberbosch, Wim J H Hagen, Yannick Schwab, David N Mastronarde. Nat Methods 2019
147
7

XDS.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
7

Model-based local density sharpening of cryo-EM maps.
Arjen J Jakobi, Matthias Wilmanns, Carsten Sachse. Elife 2017
100
6

Biochemistry. The resolution revolution.
Werner Kühlbrandt. Science 2014
564
6


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.