A citation-based method for searching scientific literature

Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
Times Cited: 10349







List of co-cited articles
187 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
56

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
53

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
38

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
33

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
29

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
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
22

How good are my data and what is the resolution?
Philip R Evans, Garib N Murshudov. Acta Crystallogr D Biol Crystallogr 2013
18

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
18

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
18

Refinement of macromolecular structures by the maximum-likelihood method.
G N Murshudov, A A Vagin, E J Dodson. Acta Crystallogr D Biol Crystallogr 1997
13

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

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
11

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
9


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


Molecular replacement with MOLREP.
Alexei Vagin, Alexei Teplyakov. Acta Crystallogr D Biol Crystallogr 2010
7

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
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
775
6

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
6



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

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.
Gerrit Langer, Serge X Cohen, Victor S Lamzin, Anastassis Perrakis. Nat Protoc 2008
5

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
5

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
5

The CCP4 suite: programs for protein crystallography.
. Acta Crystallogr D Biol Crystallogr 1994
5

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
5

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

The EMBL-EBI search and sequence analysis tools APIs in 2019.
Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R N Tivey, Simon C Potter, Robert D Finn,[...]. Nucleic Acids Res 2019
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

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
4

[20] Processing of X-ray diffraction data collected in oscillation mode.
Zbyszek Otwinowski, Wladek Minor. Methods Enzymol 1997
4

The carbohydrate-active enzymes database (CAZy) in 2013.
Vincent Lombard, Hemalatha Golaconda Ramulu, Elodie Drula, Pedro M Coutinho, Bernard Henrissat. Nucleic Acids Res 2014
4

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

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
4

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
4

Dali server: conservation mapping in 3D.
Liisa Holm, Päivi Rosenström. Nucleic Acids Res 2010
4

Clustal W and Clustal X version 2.0.
M A Larkin, G Blackshields, N P Brown, R Chenna, P A McGettigan, H McWilliam, F Valentin, I M Wallace, A Wilm, R Lopez,[...]. Bioinformatics 2007
4

A graphical user interface to the CCP4 program suite.
Elizabeth Potterton, Peter Briggs, Maria Turkenburg, Eleanor Dodson. Acta Crystallogr D Biol Crystallogr 2003
4


WebLogo: a sequence logo generator.
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
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
3

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments.
G Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Ramakrishna Annabhimoju, Woody Sherman. J Comput Aided Mol Des 2013
3

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.
Edward Harder, Wolfgang Damm, Jon Maple, Chuanjie Wu, Mark Reboul, Jin Yu Xiang, Lingle Wang, Dmitry Lupyan, Markus K Dahlgren, Jennifer L Knight,[...]. J Chem Theory Comput 2016
3

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
Ian W Davis, Andrew Leaver-Fay, Vincent B Chen, Jeremy N Block, Gary J Kapral, Xueyi Wang, Laura W Murray, W Bryan Arendall, Jack Snoeyink, Jane S Richardson,[...]. Nucleic Acids Res 2007
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.