A citation-based method for searching scientific literature

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, Airlie J McCoy, Nigel W Moriarty, Robert Oeffner, Randy J Read, David C Richardson, Jane S Richardson, Thomas C Terwilliger, Peter H Zwart. Acta Crystallogr D Biol Crystallogr 2010
Times Cited: 15707







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



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
58

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
35

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
33

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
33

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
28

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
27

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
19

[20] Processing of X-ray diffraction data collected in oscillation mode.
Zbyszek Otwinowski, Wladek Minor. Methods Enzymol 1997
19

Inference of macromolecular assemblies from crystalline state.
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
14

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
14

CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
14

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
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
10

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
10

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
9

How good are my data and what is the resolution?
Philip R Evans, Garib N Murshudov. Acta Crystallogr D Biol Crystallogr 2013
8


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
631
7

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
6

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
6



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

CASTp 3.0: computed atlas of surface topography of proteins.
Wei Tian, Chang Chen, Xue Lei, Jieling Zhao, Jie Liang. Nucleic Acids Res 2018
486
5


Scaling and assessment of data quality.
Philip Evans. Acta Crystallogr D Biol Crystallogr 2006
4



The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
4

Integration, scaling, space-group assignment and post-refinement.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
4


HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes.
Wladek Minor, Marcin Cymborowski, Zbyszek Otwinowski, Maksymilian Chruszcz. Acta Crystallogr D Biol Crystallogr 2006
4


SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Christopher O Barnes, Claudia A Jette, Morgan E Abernathy, Kim-Marie A Dam, Shannon R Esswein, Harry B Gristick, Andrey G Malyutin, Naima G Sharaf, Kathryn E Huey-Tubman, Yu E Lee,[...]. Nature 2020
577
4

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.
Wanwisa Dejnirattisai, Jiandong Huo, Daming Zhou, Jiří Zahradník, Piyada Supasa, Chang Liu, Helen M E Duyvesteyn, Helen M Ginn, Alexander J Mentzer, Aekkachai Tuekprakhon,[...]. Cell 2022
121
4

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
524
4

Development and testing of a general amber force field.
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
3

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
3

Announcing the worldwide Protein Data Bank.
Helen Berman, Kim Henrick, Haruki Nakamura. Nat Struct Biol 2003
3

The carbohydrate-active enzymes database (CAZy) in 2013.
Vincent Lombard, Hemalatha Golaconda Ramulu, Elodie Drula, Pedro M Coutinho, Bernard Henrissat. Nucleic Acids Res 2014
3

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
3

Dali server update.
Liisa Holm, Laura M Laakso. Nucleic Acids Res 2016
614
3

REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.
Alexei A Vagin, Roberto A Steiner, Andrey A Lebedev, Liz Potterton, Stuart McNicholas, Fei Long, Garib N Murshudov. Acta Crystallogr D Biol Crystallogr 2004
3

DIALS: implementation and evaluation of a new integration package.
Graeme Winter, David G Waterman, James M Parkhurst, Aaron S Brewster, Richard J Gildea, Markus Gerstel, Luis Fuentes-Montero, Melanie Vollmar, Tara Michels-Clark, Iris D Young,[...]. Acta Crystallogr D Struct Biol 2018
393
3

Software tools for automated transmission electron microscopy.
Martin Schorb, Isabella Haberbosch, Wim J H Hagen, Yannick Schwab, David N Mastronarde. Nat Methods 2019
141
3


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.