Kai Zhang. J Struct Biol 2016
Times Cited: 1784
Times Cited: 1784
Times Cited
Times Co-cited
Similarity
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
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng, David A Agard. Nat Methods 2017
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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
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
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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
Jasenko Zivanov, Takanori Nakane, Björn O Forsberg, Dari Kimanius, Wim Jh Hagen, Erik Lindahl, Sjors Hw Scheres. Elife 2018
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Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
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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
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
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Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
40
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
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RELION: implementation of a Bayesian approach to cryo-EM structure determination.
Sjors H W Scheres. J Struct Biol 2012
Sjors H W Scheres. J Struct Biol 2012
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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
Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin. Protein Sci 2018
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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
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
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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
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
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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
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
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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
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
20
Automated electron microscope tomography using robust prediction of specimen movements.
David N Mastronarde. J Struct Biol 2005
David N Mastronarde. J Struct Biol 2005
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Quantifying the local resolution of cryo-EM density maps.
Alp Kucukelbir, Fred J Sigworth, Hemant D Tagare. Nat Methods 2014
Alp Kucukelbir, Fred J Sigworth, Hemant D Tagare. Nat Methods 2014
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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
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
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Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.
Peter B Rosenthal, Richard Henderson. J Mol Biol 2003
Peter B Rosenthal, Richard Henderson. J Mol Biol 2003
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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
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
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Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1.
Jasenko Zivanov, Takanori Nakane, Sjors H W Scheres. IUCrJ 2020
Jasenko Zivanov, Takanori Nakane, Sjors H W Scheres. IUCrJ 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
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
9
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
Benjamin A Barad, Nathaniel Echols, Ray Yu-Ruei Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James S Fraser. Nat Methods 2015
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HOLE: a program for the analysis of the pore dimensions of ion channel structural models.
O S Smart, J G Neduvelil, X Wang, B A Wallace, M S Sansom. J Mol Graph 1996
O S Smart, J G Neduvelil, X Wang, B A Wallace, M S Sansom. J Mol Graph 1996
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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
Thorsten Wagner, Felipe Merino, Markus Stabrin, Toshio Moriya, Claudia Antoni, Amir Apelbaum, Philine Hagel, Oleg Sitsel, Tobias Raisch, Daniel Prumbaum,[...]. Commun Biol 2019
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
Shaoxia Chen, Greg McMullan, Abdul R Faruqi, Garib N Murshudov, Judith M Short, Sjors H W Scheres, Richard Henderson. Ultramicroscopy 2013
9
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.
Dari Kimanius, Björn O Forsberg, Sjors Hw Scheres, Erik Lindahl. Elife 2016
Dari Kimanius, Björn O Forsberg, Sjors Hw Scheres, Erik Lindahl. Elife 2016
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Prevention of overfitting in cryo-EM structure determination.
Sjors H W Scheres, Shaoxia Chen. Nat Methods 2012
Sjors H W Scheres, Shaoxia Chen. Nat Methods 2012
8
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
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
8
Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope.
Jianlin Lei, Joachim Frank. J Struct Biol 2005
Jianlin Lei, Joachim Frank. J Struct Biol 2005
8
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
Takanori Nakane, Dari Kimanius, Erik Lindahl, Sjors Hw Scheres. Elife 2018
7
Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6.
Timothy Grant, Nikolaus Grigorieff. Elife 2015
Timothy Grant, Nikolaus Grigorieff. Elife 2015
7
Conformational transitions of a neurotensin receptor 1-Gi1 complex.
Hideaki E Kato, Yan Zhang, Hongli Hu, Carl-Mikael Suomivuori, Francois Marie Ngako Kadji, Junken Aoki, Kaavya Krishna Kumar, Rasmus Fonseca, Daniel Hilger, Weijiao Huang,[...]. Nature 2019
Hideaki E Kato, Yan Zhang, Hongli Hu, Carl-Mikael Suomivuori, Francois Marie Ngako Kadji, Junken Aoki, Kaavya Krishna Kumar, Rasmus Fonseca, Daniel Hilger, Weijiao Huang,[...]. Nature 2019
7
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
Yong Zi Tan, Philip R Baldwin, Joseph H Davis, James R Williamson, Clinton S Potter, Bridget Carragher, Dmitry Lyumkis. Nat Methods 2017
7
cisTEM, user-friendly software for single-particle image processing.
Timothy Grant, Alexis Rohou, Nikolaus Grigorieff. Elife 2018
Timothy Grant, Alexis Rohou, Nikolaus Grigorieff. Elife 2018
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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
Airlie J McCoy, Ralf W Grosse-Kunstleve, Paul D Adams, Martyn D Winn, Laurent C Storoni, Randy J Read. J Appl Crystallogr 2007
7
A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis.
Jasenko Zivanov, Takanori Nakane, Sjors H W Scheres. IUCrJ 2019
Jasenko Zivanov, Takanori Nakane, Sjors H W Scheres. IUCrJ 2019
7
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
Daniel Wrapp, Nianshuang Wang, Kizzmekia S Corbett, Jory A Goldsmith, Ching-Lin Hsieh, Olubukola Abiona, Barney S Graham, Jason S McLellan. Science 2020
6
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
Nigel W Moriarty, Ralf W Grosse-Kunstleve, Paul D Adams. Acta Crystallogr D Biol Crystallogr 2009
6
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Tristan Ian Croll. Acta Crystallogr D Struct Biol 2018
Tristan Ian Croll. Acta Crystallogr D Struct Biol 2018
6
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
Tristan Bepler, Andrew Morin, Micah Rapp, Julia Brasch, Lawrence Shapiro, Alex J Noble, Bonnie Berger. Nat Methods 2019
6
Deciphering key features in protein structures with the new ENDscript server.
Xavier Robert, Patrice Gouet. Nucleic Acids Res 2014
Xavier Robert, Patrice Gouet. Nucleic Acids Res 2014
6
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
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
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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
Christian Suloway, James Pulokas, Denis Fellmann, Anchi Cheng, Francisco Guerra, Joel Quispe, Scott Stagg, Clinton S Potter, Bridget Carragher. J Struct Biol 2005
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Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7.
Pengfei Wang, Manoj S Nair, Lihong Liu, Sho Iketani, Yang Luo, Yicheng Guo, Maple Wang, Jian Yu, Baoshan Zhang, Peter D Kwong,[...]. Nature 2021
Pengfei Wang, Manoj S Nair, Lihong Liu, Sho Iketani, Yang Luo, Yicheng Guo, Maple Wang, Jian Yu, Baoshan Zhang, Peter D Kwong,[...]. Nature 2021
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Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody.
Dora Pinto, Young-Jun Park, Martina Beltramello, Alexandra C Walls, M Alejandra Tortorici, Siro Bianchi, Stefano Jaconi, Katja Culap, Fabrizia Zatta, Anna De Marco,[...]. Nature 2020
Dora Pinto, Young-Jun Park, Martina Beltramello, Alexandra C Walls, M Alejandra Tortorici, Siro Bianchi, Stefano Jaconi, Katja Culap, Fabrizia Zatta, Anna De Marco,[...]. Nature 2020
5
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
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
5
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
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
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Processing of Structurally Heterogeneous Cryo-EM Data in RELION.
S H W Scheres. Methods Enzymol 2016
S H W Scheres. Methods Enzymol 2016
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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
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
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.