A citation-based method for searching scientific literature

P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
Times Cited: 14682







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



Times Cited
  Times     Co-cited
Similarity


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
41

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
34

XDS.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
34

Phaser crystallographic software.
Airlie J McCoy, Ralf W Grosse-Kunstleve, Paul D Adams, Martyn D Winn, Laurent C Storoni, Randy J Read. J Appl Crystallogr 2007
34

Overview of the CCP4 suite and current developments.
Martyn D Winn, Charles C Ballard, Kevin D Cowtan, Eleanor J Dodson, Paul Emsley, Phil R Evans, Ronan M Keegan, Eugene B Krissinel, Andrew G W Leslie, Airlie McCoy,[...]. Acta Crystallogr D Biol Crystallogr 2011
23

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
22

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
19

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
18

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
18

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

How good are my data and what is the resolution?
Philip R Evans, Garib N Murshudov. Acta Crystallogr D Biol Crystallogr 2013
14

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
14

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
13


Inference of macromolecular assemblies from crystalline state.
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
12

Towards automated crystallographic structure refinement with phenix.refine.
Pavel V Afonine, Ralf W Grosse-Kunstleve, Nathaniel Echols, Jeffrey J Headd, Nigel W Moriarty, Marat Mustyakimov, Thomas C Terwilliger, Alexandre Urzhumtsev, Peter H Zwart, Paul D Adams. Acta Crystallogr D Biol Crystallogr 2012
12


[20] Processing of X-ray diffraction data collected in oscillation mode.
Zbyszek Otwinowski, Wladek Minor. Methods Enzymol 1997
11

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
10

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
709
10

CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
10



Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
8


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
209
7

NMRPipe: a multidimensional spectral processing system based on UNIX pipes.
F Delaglio, S Grzesiek, G W Vuister, G Zhu, J Pfeifer, A Bax. J Biomol NMR 1995
7

Refinement of macromolecular structures by the maximum-likelihood method.
G N Murshudov, A A Vagin, E J Dodson. Acta Crystallogr D Biol Crystallogr 1997
7

Data processing and analysis with the autoPROC toolbox.
Clemens Vonrhein, Claus Flensburg, Peter Keller, Andrew Sharff, Oliver Smart, Wlodek Paciorek, Thomas Womack, Gérard Bricogne. Acta Crystallogr D Biol Crystallogr 2011
689
7

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
6

iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM.
T Geoff G Battye, Luke Kontogiannis, Owen Johnson, Harold R Powell, Andrew G W Leslie. Acta Crystallogr D Biol Crystallogr 2011
6

Quantifying the local resolution of cryo-EM density maps.
Alp Kucukelbir, Fred J Sigworth, Hemant D Tagare. Nat Methods 2014
5



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
5

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
5

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
5

Scaling and assessment of data quality.
Philip Evans. Acta Crystallogr D Biol Crystallogr 2006
5

Molecular replacement with MOLREP.
Alexei Vagin, Alexei Teplyakov. Acta Crystallogr D Biol Crystallogr 2010
5

electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation.
Nigel W Moriarty, Ralf W Grosse-Kunstleve, Paul D Adams. Acta Crystallogr D Biol Crystallogr 2009
602
5

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
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
4

A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis.
Jasenko Zivanov, Takanori Nakane, Sjors H W Scheres. IUCrJ 2019
203
4

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
4

A pneumonia outbreak associated with a new coronavirus of probable bat origin.
Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang,[...]. Nature 2020
4


A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2.
Rui Shi, Chao Shan, Xiaomin Duan, Zhihai Chen, Peipei Liu, Jinwen Song, Tao Song, Xiaoshan Bi, Chao Han, Lianao Wu,[...]. Nature 2020
520
4

Real-time cryo-electron microscopy data preprocessing with Warp.
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
185
4

Polder maps: improving OMIT maps by excluding bulk solvent.
Dorothee Liebschner, Pavel V Afonine, Nigel W Moriarty, Billy K Poon, Oleg V Sobolev, Thomas C Terwilliger, Paul D Adams. Acta Crystallogr D Struct Biol 2017
271
4

Structural basis of a shared antibody response to SARS-CoV-2.
Meng Yuan, Hejun Liu, Nicholas C Wu, Chang-Chun D Lee, Xueyong Zhu, Fangzhu Zhao, Deli Huang, Wenli Yu, Yuanzi Hua, Henry Tien,[...]. Science 2020
195
4


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.