A citation-based method for searching scientific literature

Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
Times Cited: 6406







List of co-cited articles
367 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
37

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
28

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
26

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
26

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
23

XDS.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
20

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
20

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
18

[20] Processing of X-ray diffraction data collected in oscillation mode.
Zbyszek Otwinowski, Wladek Minor. Methods Enzymol 1997
16

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
14

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

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
12

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
11

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
11


How good are my data and what is the resolution?
Philip R Evans, Garib N Murshudov. Acta Crystallogr D Biol Crystallogr 2013
10

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
9

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
8

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
944
8

Scaling and assessment of data quality.
Philip Evans. Acta Crystallogr D Biol Crystallogr 2006
8


Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil.
Nuno R Faria, Thomas A Mellan, Charles Whittaker, Ingra M Claro, Darlan da S Candido, Swapnil Mishra, Myuki A E Crispim, Flavia C S Sales, Iwona Hawryluk, John T McCrone,[...]. Science 2021
531
7

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

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift.
Elisabetta Cameroni, John E Bowen, Laura E Rosen, Christian Saliba, Samantha K Zepeda, Katja Culap, Dora Pinto, Laura A VanBlargan, Anna De Marco, Julia di Iulio,[...]. Nature 2022
195
7

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
7

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
7

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
890
6

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
6

Refinement of macromolecular structures by the maximum-likelihood method.
G N Murshudov, A A Vagin, E J Dodson. Acta Crystallogr D Biol Crystallogr 1997
6

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
6

Potently neutralizing and protective human antibodies against SARS-CoV-2.
Seth J Zost, Pavlo Gilchuk, James Brett Case, Elad Binshtein, Rita E Chen, Joseph P Nkolola, Alexandra Schäfer, Joseph X Reidy, Andrew Trivette, Rachel S Nargi,[...]. Nature 2020
547
6

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.
M Alejandra Tortorici, Martina Beltramello, Florian A Lempp, Dora Pinto, Ha V Dang, Laura E Rosen, Matthew McCallum, John Bowen, Andrea Minola, Stefano Jaconi,[...]. Science 2020
292
6


Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies.
Yunlong Cao, Jing Wang, Fanchong Jian, Tianhe Xiao, Weiliang Song, Ayijiang Yisimayi, Weijin Huang, Qianqian Li, Peng Wang, Ran An,[...]. Nature 2022
198
6


Jalview Version 2--a multiple sequence alignment editor and analysis workbench.
Andrew M Waterhouse, James B Procter, David M A Martin, Michèle Clamp, Geoffrey J Barton. Bioinformatics 2009
5

Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody.
C Garrett Rappazzo, Longping V Tse, Chengzi I Kaku, Daniel Wrapp, Mrunal Sakharkar, Deli Huang, Laura M Deveau, Thomas J Yockachonis, Andrew S Herbert, Michael B Battles,[...]. Science 2021
130
5

Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.
Gabriele Cerutti, Yicheng Guo, Tongqing Zhou, Jason Gorman, Myungjin Lee, Micah Rapp, Eswar R Reddem, Jian Yu, Fabiana Bahna, Jude Bimela,[...]. Cell Host Microbe 2021
193
5

Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike.
Lihong Liu, Pengfei Wang, Manoj S Nair, Jian Yu, Micah Rapp, Qian Wang, Yang Luo, Jasper F-W Chan, Vincent Sahi, Amir Figueroa,[...]. Nature 2020
765
5

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
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


Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail.
Johanna Hansen, Alina Baum, Kristen E Pascal, Vincenzo Russo, Stephanie Giordano, Elzbieta Wloga, Benjamin O Fulton, Ying Yan, Katrina Koon, Krunal Patel,[...]. Science 2020
644
5

Convergent antibody responses to SARS-CoV-2 in convalescent individuals.
Davide F Robbiani, Christian Gaebler, Frauke Muecksch, Julio C C Lorenzi, Zijun Wang, Alice Cho, Marianna Agudelo, Christopher O Barnes, Anna Gazumyan, Shlomo Finkin,[...]. Nature 2020
5

In vitro and in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies.
Dapeng Li, Robert J Edwards, Kartik Manne, David R Martinez, Alexandra Schäfer, S Munir Alam, Kevin Wiehe, Xiaozhi Lu, Robert Parks, Laura L Sutherland,[...]. Cell 2021
80
6

PHENIX: building new software for automated crystallographic structure determination.
Paul D Adams, Ralf W Grosse-Kunstleve, Li Wei Hung, Thomas R Ioerger, Airlie J McCoy, Nigel W Moriarty, Randy J Read, James C Sacchettini, Nicholas K Sauter, Thomas C Terwilliger. Acta Crystallogr D Biol Crystallogr 2002
5

Structural basis of a shared antibody response to SARS-CoV-2.
Meng Yuan, Hejun Liu, Nicholas C Wu, Chang-Chun D Lee, Xueyong Zhu, Fangzhu Zhao, Deli Huang, Wenli Yu, Yuanzi Hua, Henry Tien,[...]. Science 2020
294
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

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
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.