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, Nigel W Moriarty, Robert D Oeffner, Billy K Poon, Michael G Prisant, Randy J Read, Jane S Richardson, David C Richardson, Massimo D Sammito, Oleg V Sobolev, Duncan H Stockwell, Thomas C Terwilliger, Alexandre G Urzhumtsev, Lizbeth L Videau, Christopher J Williams, Paul D Adams. Acta Crystallogr D Struct Biol 2019
Times Cited: 1374
Times Cited: 1374
Times Cited
Times Co-cited
Similarity
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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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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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
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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
24
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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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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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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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
19
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 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: 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
16
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
15
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
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
Inference of macromolecular assemblies from crystalline state.
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
14
[20] Processing of X-ray diffraction data collected in oscillation mode.
Zbyszek Otwinowski, Wladek Minor. Methods Enzymol 1997
Zbyszek Otwinowski, Wladek Minor. Methods Enzymol 1997
11
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
9
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
9
CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
9
How good are my data and what is the resolution?
Philip R Evans, Garib N Murshudov. Acta Crystallogr D Biol Crystallogr 2013
Philip R Evans, Garib N Murshudov. Acta Crystallogr D Biol Crystallogr 2013
8
Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction.
Ali Punjani, Haowei Zhang, David J Fleet. Nat Methods 2020
Ali Punjani, Haowei Zhang, David J Fleet. Nat Methods 2020
8
Current developments in Coot for macromolecular model building of Electron Cryo-microscopy and Crystallographic Data.
Ana Casañal, Bernhard Lohkamp, Paul Emsley. Protein Sci 2020
Ana Casañal, Bernhard Lohkamp, Paul Emsley. Protein Sci 2020
8
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
8
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
7
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
7
Processing of X-ray diffraction data collected in oscillation mode.
Z Otwinowski, W Minor. Methods Enzymol 1997
Z Otwinowski, W Minor. Methods Enzymol 1997
7
Automated electron microscope tomography using robust prediction of specimen movements.
David N Mastronarde. J Struct Biol 2005
David N Mastronarde. J Struct Biol 2005
7
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
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
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
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
6
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
6
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
5
Molecular replacement with MOLREP.
Alexei Vagin, Alexei Teplyakov. Acta Crystallogr D Biol Crystallogr 2010
Alexei Vagin, Alexei Teplyakov. Acta Crystallogr D Biol Crystallogr 2010
5
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
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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
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
5
Real-time cryo-electron microscopy data preprocessing with Warp.
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
5
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
5
Structure-based design of prefusion-stabilized SARS-CoV-2 spikes.
Ching-Lin Hsieh, Jory A Goldsmith, Jeffrey M Schaub, Andrea M DiVenere, Hung-Che Kuo, Kamyab Javanmardi, Kevin C Le, Daniel Wrapp, Alison G Lee, Yutong Liu,[...]. Science 2020
Ching-Lin Hsieh, Jory A Goldsmith, Jeffrey M Schaub, Andrea M DiVenere, Hung-Che Kuo, Kamyab Javanmardi, Kevin C Le, Daniel Wrapp, Alison G Lee, Yutong Liu,[...]. Science 2020
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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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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
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3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM.
Ali Punjani, David J Fleet. J Struct Biol 2021
Ali Punjani, David J Fleet. J Struct Biol 2021
5
Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning.
Chad W Hopkins, Scott Le Grand, Ross C Walker, Adrian E Roitberg. J Chem Theory Comput 2015
Chad W Hopkins, Scott Le Grand, Ross C Walker, Adrian E Roitberg. J Chem Theory Comput 2015
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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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CHARMM36m: an improved force field for folded and intrinsically disordered proteins.
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L de Groot, Helmut Grubmüller, Alexander D MacKerell. Nat Methods 2017
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L de Groot, Helmut Grubmüller, Alexander D MacKerell. Nat Methods 2017
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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
F Delaglio, S Grzesiek, G W Vuister, G Zhu, J Pfeifer, A Bax. J Biomol NMR 1995
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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
Alexandra C Walls, Young-Jun Park, M Alejandra Tortorici, Abigail Wall, Andrew T McGuire, David Veesler. Cell 2020
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.