A citation-based method for searching scientific literature

Yana Rose, Jose M Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, Charmi Bhikadiya, Li Chen, Alexander S Rose, Sebastian Bittrich, Stephen K Burley, John D Westbrook. J Mol Biol 2021
Times Cited: 22







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



Times Cited
  Times     Co-cited
Similarity


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
31


DrugBank 5.0: a major update to the DrugBank database for 2018.
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda,[...]. Nucleic Acids Res 2018
31


RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.
Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V Crichlow, Cole H Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M Duarte,[...]. Nucleic Acids Res 2021
246
27

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
Jasmine Y Young, John D Westbrook, Zukang Feng, Raul Sala, Ezra Peisach, Thomas J Oldfield, Sanchayita Sen, Aleksandras Gutmanas, David R Armstrong, John M Berrisford,[...]. Structure 2017
74
22

Validation of Structures in the Protein Data Bank.
Swanand Gore, Eduardo Sanz García, Pieter M S Hendrickx, Aleksandras Gutmanas, John D Westbrook, Huanwang Yang, Zukang Feng, Kumaran Baskaran, John M Berrisford, Brian P Hudson,[...]. Structure 2017
109
22

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.
John D Westbrook, Chenghua Shao, Zukang Feng, Marina Zhuravleva, Sameer Velankar, Jasmine Young. Bioinformatics 2015
77
22

The FAIR Guiding Principles for scientific data management and stewardship.
Mark D Wilkinson, Michel Dumontier, I Jsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E Bourne,[...]. Sci Data 2016
22


Announcing the worldwide Protein Data Bank.
Helen Berman, Kim Henrick, Haruki Nakamura. Nat Struct Biol 2003
22

RCSB Protein Data Bank: Enabling biomedical research and drug discovery.
David S Goodsell, Christine Zardecki, Luigi Di Costanzo, Jose M Duarte, Brian P Hudson, Irina Persikova, Joan Segura, Chenghua Shao, Maria Voigt, John D Westbrook,[...]. Protein Sci 2020
96
22

Impact of the Protein Data Bank on antineoplastic approvals.
John D Westbrook, Rose Soskind, Brian P Hudson, Stephen K Burley. Drug Discov Today 2020
13
38

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.
Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M Duarte, Shuchismita Dutta,[...]. Nucleic Acids Res 2019
489
22

BioMagResBank.
Eldon L Ulrich, Hideo Akutsu, Jurgen F Doreleijers, Yoko Harano, Yannis E Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller,[...]. Nucleic Acids Res 2008
18

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield,[...]. Database (Oxford) 2018
31
18

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.
Zukang Feng, John D Westbrook, Raul Sala, Oliver S Smart, Gérard Bricogne, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya, Kiyoko F Aoki-Kinoshita, Jeffrey C Hoch,[...]. Structure 2021
10
40


Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.
David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose. Nucleic Acids Res 2021
113
18

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
13

PDBe: improved findability of macromolecular structure data in the PDB.
David R Armstrong, John M Berrisford, Matthew J Conroy, Aleksandras Gutmanas, Stephen Anyango, Preeti Choudhary, Alice R Clark, Jose M Dana, Mandar Deshpande, Roisin Dunlop,[...]. Nucleic Acids Res 2020
51
13

A new generation of crystallographic validation tools for the protein data bank.
Randy J Read, Paul D Adams, W Bryan Arendall, Axel T Brunger, Paul Emsley, Robbie P Joosten, Gerard J Kleywegt, Eugene B Krissinel, Thomas Lütteke, Zbyszek Otwinowski,[...]. Structure 2011
305
13

Retrieval of crystallographically-derived molecular geometry information.
Ian J Bruno, Jason C Cole, Magnus Kessler, Jie Luo, W D Sam Motherwell, Lucy H Purkis, Barry R Smith, Robin Taylor, Richard I Cooper, Stephanie E Harris,[...]. J Chem Inf Comput Sci 2004
347
13

Remediation of the protein data bank archive.
Kim Henrick, Zukang Feng, Wolfgang F Bluhm, Dimitris Dimitropoulos, Jurgen F Doreleijers, Shuchismita Dutta, Judith L Flippen-Anderson, John Ionides, Chisa Kamada, Eugene Krissinel,[...]. Nucleic Acids Res 2008
106
13

The Cambridge Structural Database.
Colin R Groom, Ian J Bruno, Matthew P Lightfoot, Suzanna C Ward. Acta Crystallogr B Struct Sci Cryst Eng Mater 2016
13

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.
Shuchismita Dutta, Dimitris Dimitropoulos, Zukang Feng, Irina Persikova, Sanchayita Sen, Chenghua Shao, John Westbrook, Jasmine Young, Marina A Zhuravleva, Gerard J Kleywegt,[...]. Biopolymers 2014
25
13

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.
Saqib Mir, Younes Alhroub, Stephen Anyango, David R Armstrong, John M Berrisford, Alice R Clark, Matthew J Conroy, Jose M Dana, Mandar Deshpande, Deepti Gupta,[...]. Nucleic Acids Res 2018
53
13

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).
Akira R Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata,[...]. Protein Sci 2018
44
13

Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive.
Chenghua Shao, Huanwang Yang, John D Westbrook, Jasmine Y Young, Christine Zardecki, Stephen K Burley. Structure 2017
23
13

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Jose M Dana, Aleksandras Gutmanas, Nidhi Tyagi, Guoying Qi, Claire O'Donovan, Maria Martin, Sameer Velankar. Nucleic Acids Res 2019
66
13


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
13

The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures.
Antonina Andreeva, Eugene Kulesha, Julian Gough, Alexey G Murzin. Nucleic Acids Res 2020
71
13

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors.
Zhenming Jin, Xiaoyu Du, Yechun Xu, Yongqiang Deng, Meiqin Liu, Yao Zhao, Bing Zhang, Xiaofeng Li, Leike Zhang, Chao Peng,[...]. Nature 2020
13

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
13



Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
Alice Douangamath, Daren Fearon, Paul Gehrtz, Tobias Krojer, Petra Lukacik, C David Owen, Efrat Resnick, Claire Strain-Damerell, Anthony Aimon, Péter Ábrányi-Balogh,[...]. Nat Commun 2020
160
9

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic.
Joseph H Lubin, Christine Zardecki, Elliott M Dolan, Changpeng Lu, Zhuofan Shen, Shuchismita Dutta, John D Westbrook, Brian P Hudson, David S Goodsell, Jonathan K Williams,[...]. bioRxiv 2020
17
11

Representation of viruses in the remediated PDB archive.
Catherine L Lawson, Shuchismita Dutta, John D Westbrook, Kim Henrick, Helen M Berman. Acta Crystallogr D Biol Crystallogr 2008
28
9


Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.
Akira R Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura. Nucleic Acids Res 2017
61
9

Outcome of the first electron microscopy validation task force meeting.
Richard Henderson, Andrej Sali, Matthew L Baker, Bridget Carragher, Batsal Devkota, Kenneth H Downing, Edward H Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff,[...]. Structure 2012
296
9

Recommendations of the wwPDB NMR Validation Task Force.
Gaetano T Montelione, Michael Nilges, Ad Bax, Peter Güntert, Torsten Herrmann, Jane S Richardson, Charles D Schwieters, Wim F Vranken, Geerten W Vuister, David S Wishart,[...]. Structure 2013
107
9

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Paul D Adams, Kathleen Aertgeerts, Cary Bauer, Jeffrey A Bell, Helen M Berman, Talapady N Bhat, Jeff M Blaney, Evan Bolton, Gerard Bricogne, David Brown,[...]. Structure 2016
44
9

Approaches to target tractability assessment - a practical perspective.
Kristin K Brown, Michael M Hann, Ami S Lakdawala, Rita Santos, Pamela J Thomas, Kieran Todd. Medchemcomm 2018
22
9


RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education.
Stephen K Burley, Helen M Berman, Cole Christie, Jose M Duarte, Zukang Feng, John Westbrook, Jasmine Young, Christine Zardecki. Protein Sci 2018
119
9

MPTherm-pred: Analysis and Prediction of Thermal Stability Changes upon Mutations in Transmembrane Proteins.
A Kulandaisamy, Jan Zaucha, Dmitrij Frishman, M Michael Gromiha. J Mol Biol 2021
5
40

GlyTouCan: an accessible glycan structure repository.
Michael Tiemeyer, Kazuhiro Aoki, James Paulson, Richard D Cummings, William S York, Niclas G Karlsson, Frederique Lisacek, Nicolle H Packer, Matthew P Campbell, Nobuyuki P Aoki,[...]. Glycobiology 2017
80
9


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.