A citation-based method for searching scientific literature

Philip R Evans, Garib N Murshudov. Acta Crystallogr D Biol Crystallogr 2013
Times Cited: 2471







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



Times Cited
  Times     Co-cited
Similarity


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
65

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
64

XDS.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
58

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
44

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
34

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
32

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
26

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
25

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
25

Inference of macromolecular assemblies from crystalline state.
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
22

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
20

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
18

Scaling and assessment of data quality.
Philip Evans. Acta Crystallogr D Biol Crystallogr 2006
15

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
775
14

Integration, scaling, space-group assignment and post-refinement.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
13

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
13

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
11

Molecular replacement with MOLREP.
Alexei Vagin, Alexei Teplyakov. Acta Crystallogr D Biol Crystallogr 2010
9

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
9



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

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
7

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
679
7

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
7

The PDB_REDO server for macromolecular structure model optimization.
Robbie P Joosten, Fei Long, Garib N Murshudov, Anastassis Perrakis. IUCrJ 2014
457
7

Linking crystallographic model and data quality.
P Andrew Karplus, Kay Diederichs. Science 2012
7

The CCP4 suite: programs for protein crystallography.
. Acta Crystallogr D Biol Crystallogr 1994
6

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.
Thomas C Terwilliger, Ralf W Grosse-Kunstleve, Pavel V Afonine, Nigel W Moriarty, Peter H Zwart, Li Wei Hung, Randy J Read, Paul D Adams. Acta Crystallogr D Biol Crystallogr 2008
6

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
6

MX2: a high-flux undulator microfocus beamline serving both the chemical and macromolecular crystallography communities at the Australian Synchrotron.
David Aragão, Jun Aishima, Hima Cherukuvada, Robert Clarken, Mark Clift, Nathan Philip Cowieson, Daniel Jesper Ericsson, Christine L Gee, Sofia Macedo, Nathan Mudie,[...]. J Synchrotron Radiat 2018
126
6

WebLogo: a sequence logo generator.
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
6

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
5

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
5

ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions.
D Franke, M V Petoukhov, P V Konarev, A Panjkovich, A Tuukkanen, H D T Mertens, A G Kikhney, N R Hajizadeh, J M Franklin, C M Jeffries,[...]. J Appl Crystallogr 2017
694
5

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
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
5

Using Dali for Protein Structure Comparison.
Liisa Holm. Methods Mol Biol 2020
90
5

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
5


SignalP 5.0 improves signal peptide predictions using deep neural networks.
José Juan Almagro Armenteros, Konstantinos D Tsirigos, Casper Kaae Sønderby, Thomas Nordahl Petersen, Ole Winther, Søren Brunak, Gunnar von Heijne, Henrik Nielsen. Nat Biotechnol 2019
4

Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines.
Timothy M McPhillips, Scott E McPhillips, Hsiu-Ju Chiu, Aina E Cohen, Ashley M Deacon, Paul J Ellis, Elspeth Garman, Ana Gonzalez, Nicholas K Sauter, R Paul Phizackerley,[...]. J Synchrotron Radiat 2002
700
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
315
4

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.
Woonghee Lee, Marco Tonelli, John L Markley. Bioinformatics 2015
846
4


MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
4

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.
Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
4

Presenting your structures: the CCP4mg molecular-graphics software.
S McNicholas, E Potterton, K S Wilson, M E M Noble. Acta Crystallogr D Biol Crystallogr 2011
878
4

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
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.