A citation-based method for searching scientific literature

Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, Evan E Bolton. Nucleic Acids Res 2019
Times Cited: 865







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



Times Cited
  Times     Co-cited
Similarity


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
24


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
12

ZINC 15--Ligand Discovery for Everyone.
Teague Sterling, John J Irwin. J Chem Inf Model 2015
843
12

Open Babel: An open chemical toolbox.
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison. J Cheminform 2011
12

ChEMBL: towards direct deposition of bioassay data.
David Mendez, Anna Gaulton, A Patrícia Bento, Jon Chambers, Marleen De Veij, Eloy Félix, María Paula Magariños, Juan F Mosquera, Prudence Mutowo, Michal Nowotka,[...]. Nucleic Acids Res 2019
250
10

The ChEMBL database in 2017.
Anna Gaulton, Anne Hersey, Michał Nowotka, A Patrícia Bento, Jon Chambers, David Mendez, Prudence Mutowo, Francis Atkinson, Louisa J Bellis, Elena Cibrián-Uhalte,[...]. Nucleic Acids Res 2017
736
9


HMDB 4.0: the human metabolome database for 2018.
David S Wishart, Yannick Djoumbou Feunang, Ana Marcu, An Chi Guo, Kevin Liang, Rosa Vázquez-Fresno, Tanvir Sajed, Daniel Johnson, Carin Li, Naama Karu,[...]. Nucleic Acids Res 2018
8

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
7

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
7

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
David E Gordon, Gwendolyn M Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M White, Matthew J O'Meara, Veronica V Rezelj, Jeffrey Z Guo, Danielle L Swaney,[...]. Nature 2020
7

Extended-connectivity fingerprints.
David Rogers, Mathew Hahn. J Chem Inf Model 2010
7

PubChem Substance and Compound databases.
Sunghwan Kim, Paul A Thiessen, Evan E Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han, Jane He, Siqian He, Benjamin A Shoemaker,[...]. Nucleic Acids Res 2016
7

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
7

The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
Justin Lamb, Emily D Crawford, David Peck, Joshua W Modell, Irene C Blat, Matthew J Wrobel, Jim Lerner, Jean-Philippe Brunet, Aravind Subramanian, Kenneth N Ross,[...]. Science 2006
6

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
6

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.
Richard A Friesner, Jay L Banks, Robert B Murphy, Thomas A Halgren, Jasna J Klicic, Daniel T Mainz, Matthew P Repasky, Eric H Knoll, Mee Shelley, Jason K Perry,[...]. J Med Chem 2004
6

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.
Markus Hoffmann, Hannah Kleine-Weber, Simon Schroeder, Nadine Krüger, Tanja Herrler, Sandra Erichsen, Tobias S Schiergens, Georg Herrler, Nai-Huei Wu, Andreas Nitsche,[...]. Cell 2020
6

DrugBank: a comprehensive resource for in silico drug discovery and exploration.
David S Wishart, Craig Knox, An Chi Guo, Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, Jennifer Woolsey. Nucleic Acids Res 2006
6

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.
Michael K Gilson, Tiqing Liu, Michael Baitaluk, George Nicola, Linda Hwang, Jenny Chong. Nucleic Acids Res 2016
378
5

Machine learning in chemoinformatics and drug discovery.
Yu-Chen Lo, Stefano E Rensi, Wen Torng, Russ B Altman. Drug Discov Today 2018
221
5

Small-molecule library screening by docking with PyRx.
Sargis Dallakyan, Arthur J Olson. Methods Mol Biol 2015
495
5

The SIDER database of drugs and side effects.
Michael Kuhn, Ivica Letunic, Lars Juhl Jensen, Peer Bork. Nucleic Acids Res 2016
326
5

The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY.
Jane F Armstrong, Elena Faccenda, Simon D Harding, Adam J Pawson, Christopher Southan, Joanna L Sharman, Brice Campo, David R Cavanagh, Stephen P H Alexander, Anthony P Davenport,[...]. Nucleic Acids Res 2020
69
7



TCMSP: a database of systems pharmacology for drug discovery from herbal medicines.
Jinlong Ru, Peng Li, Jinan Wang, Wei Zhou, Bohui Li, Chao Huang, Pidong Li, Zihu Guo, Weiyang Tao, Yinfeng Yang,[...]. J Cheminform 2014
903
5

The Comparative Toxicogenomics Database: update 2019.
Allan Peter Davis, Cynthia J Grondin, Robin J Johnson, Daniela Sciaky, Roy McMorran, Jolene Wiegers, Thomas C Wiegers, Carolyn J Mattingly. Nucleic Acids Res 2019
320
5

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
5

Identifying small molecules via high resolution mass spectrometry: communicating confidence.
Emma L Schymanski, Junho Jeon, Rebekka Gulde, Kathrin Fenner, Matthias Ruff, Heinz P Singer, Juliane Hollender. Environ Sci Technol 2014
914
5

GROMACS: fast, flexible, and free.
David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, Herman J C Berendsen. J Comput Chem 2005
4

SwissTargetPrediction: a web server for target prediction of bioactive small molecules.
David Gfeller, Aurélien Grosdidier, Matthias Wirth, Antoine Daina, Olivier Michielin, Vincent Zoete. Nucleic Acids Res 2014
334
4

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
4

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.
Aravind Subramanian, Rajiv Narayan, Steven M Corsello, David D Peck, Ted E Natoli, Xiaodong Lu, Joshua Gould, John F Davis, Andrew A Tubelli, Jacob K Asiedu,[...]. Cell 2017
777
4

ChEBI in 2016: Improved services and an expanding collection of metabolites.
Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck. Nucleic Acids Res 2016
259
4

The Protein Data Bank.
Helen M Berman, Tammy Battistuz, T N Bhat, Wolfgang F Bluhm, Philip E Bourne, Kyle Burkhardt, Zukang Feng, Gary L Gilliland, Lisa Iype, Shri Jain,[...]. Acta Crystallogr D Biol Crystallogr 2002
4

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
4

The Drug Repurposing Hub: a next-generation drug library and information resource.
Steven M Corsello, Joshua A Bittker, Zihan Liu, Joshua Gould, Patrick McCarren, Jodi E Hirschman, Stephen E Johnston, Anita Vrcic, Bang Wong, Mariya Khan,[...]. Nat Med 2017
268
4

Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2.
Yadi Zhou, Yuan Hou, Jiayu Shen, Yin Huang, William Martin, Feixiong Cheng. Cell Discov 2020
587
4

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
4

Reoptimization of MDL keys for use in drug discovery.
Joseph L Durant, Burton A Leland, Douglas R Henry, James G Nourse. J Chem Inf Comput Sci 2002
504
4

MetFrag relaunched: incorporating strategies beyond in silico fragmentation.
Christoph Ruttkies, Emma L Schymanski, Sebastian Wolf, Juliane Hollender, Steffen Neumann. J Cheminform 2016
325
4

The ChEMBL bioactivity database: an update.
A Patrícia Bento, Anna Gaulton, Anne Hersey, Louisa J Bellis, Jon Chambers, Mark Davies, Felix A Krüger, Yvonne Light, Lora Mak, Shaun McGlinchey,[...]. Nucleic Acids Res 2014
848
4

MassBank: a public repository for sharing mass spectral data for life sciences.
Hisayuki Horai, Masanori Arita, Shigehiko Kanaya, Yoshito Nihei, Tasuku Ikeda, Kazuhiro Suwa, Yuya Ojima, Kenichi Tanaka, Satoshi Tanaka, Ken Aoshima,[...]. J Mass Spectrom 2010
946
4

Drug repurposing: progress, challenges and recommendations.
Sudeep Pushpakom, Francesco Iorio, Patrick A Eyers, K Jane Escott, Shirley Hopper, Andrew Wells, Andrew Doig, Tim Guilliams, Joanna Latimer, Christine McNamee,[...]. Nat Rev Drug Discov 2019
871
4

Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17.
Lars Ruddigkeit, Ruud van Deursen, Lorenz C Blum, Jean-Louis Reymond. J Chem Inf Model 2012
325
4

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
4

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
P A Kollman, I Massova, C Reyes, B Kuhn, S Huo, L Chong, M Lee, T Lee, Y Duan, W Wang,[...]. Acc Chem Res 2000
3

Estimation of the size of drug-like chemical space based on GDB-17 data.
P G Polishchuk, T I Madzhidov, A Varnek. J Comput Aided Mol Des 2013
108
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.