A citation-based method for searching scientific literature

Sunghwan Kim, Paul A Thiessen, Evan E Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han, Jane He, Siqian He, Benjamin A Shoemaker, Jiyao Wang, Bo Yu, Jian Zhang, Stephen H Bryant. Nucleic Acids Res 2016
Times Cited: 1779







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



Times Cited
  Times     Co-cited
Similarity



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
15

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
15


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
11

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
11

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
9

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
9

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
9

Lead- and drug-like compounds: the rule-of-five revolution.
Christopher A Lipinski. Drug Discov Today Technol 2004
7

Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.
Hyuna Sung, Jacques Ferlay, Rebecca L Siegel, Mathieu Laversanne, Isabelle Soerjomataram, Ahmedin Jemal, Freddie Bray. CA Cancer J Clin 2021
7

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

ChEMBL: a large-scale bioactivity database for drug discovery.
Anna Gaulton, Louisa J Bellis, A Patricia Bento, Jon Chambers, Mark Davies, Anne Hersey, Yvonne Light, Shaun McGlinchey, David Michalovich, Bissan Al-Lazikani,[...]. Nucleic Acids Res 2012
6



Development and testing of a general amber force field.
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
5

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
5

Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.
Richard A Friesner, Robert B Murphy, Matthew P Repasky, Leah L Frye, Jeremy R Greenwood, Thomas A Halgren, Paul C Sanschagrin, Daniel T Mainz. J Med Chem 2006
5

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
406
5

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities.
Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N Jorissen, Michael K Gilson. Nucleic Acids Res 2007
959
5

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
5

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.
Alexander W Schüttelkopf, Daan M F van Aalten. Acta Crystallogr D Biol Crystallogr 2004
5

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
5


Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.
Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Alireza Hadj Khodabakhshi, Olga Tanaseichuk, Christopher Benner, Sumit K Chanda. Nat Commun 2019
5

PubChem 2019 update: improved access to chemical data.
Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu,[...]. Nucleic Acids Res 2019
5

BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine.
Zhongyang Liu, Feifei Guo, Yong Wang, Chun Li, Xinlei Zhang, Honglei Li, Lihong Diao, Jiangyong Gu, Wei Wang, Dong Li,[...]. Sci Rep 2016
272
5

Molecular properties that influence the oral bioavailability of drug candidates.
Daniel F Veber, Stephen R Johnson, Hung-Yuan Cheng, Brian R Smith, Keith W Ward, Kenneth D Kopple. J Med Chem 2002
4

Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.
Thomas A Halgren, Robert B Murphy, Richard A Friesner, Hege S Beard, Leah L Frye, W Thomas Pollard, Jay L Banks. J Med Chem 2004
4

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.
Chaolin Huang, Yeming Wang, Xingwang Li, Lili Ren, Jianping Zhao, Yi Hu, Li Zhang, Guohui Fan, Jiuyang Xu, Xiaoying Gu,[...]. Lancet 2020
4

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
4


Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution.
Jeremy R Greenwood, David Calkins, Arron P Sullivan, John C Shelley. J Comput Aided Mol Des 2010
424
4

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
4

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors.
Linlin Zhang, Daizong Lin, Xinyuanyuan Sun, Ute Curth, Christian Drosten, Lucie Sauerhering, Stephan Becker, Katharina Rox, Rolf Hilgenfeld. Science 2020
4


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

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
4

Development and validation of a genetic algorithm for flexible docking.
G Jones, P Willett, R C Glen, A R Leach, R Taylor. J Mol Biol 1997
4

The SIDER database of drugs and side effects.
Michael Kuhn, Ivica Letunic, Lars Juhl Jensen, Peer Bork. Nucleic Acids Res 2016
370
4


Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks.
Marwin H S Segler, Thierry Kogej, Christian Tyrchan, Mark P Waller. ACS Cent Sci 2018
344
4

Deep reinforcement learning for de novo drug design.
Mariya Popova, Olexandr Isayev, Alexander Tropsha. Sci Adv 2018
255
4

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules.
Rafael Gómez-Bombarelli, Jennifer N Wei, David Duvenaud, José Miguel Hernández-Lobato, Benjamín Sánchez-Lengeling, Dennis Sheberla, Jorge Aguilera-Iparraguirre, Timothy D Hirzel, Ryan P Adams, Alán Aspuru-Guzik. ACS Cent Sci 2018
565
4

Molecular de-novo design through deep reinforcement learning.
Marcus Olivecrona, Thomas Blaschke, Ola Engkvist, Hongming Chen. J Cheminform 2017
242
4

Fréchet ChemNet Distance: A Metric for Generative Models for Molecules in Drug Discovery.
Kristina Preuer, Philipp Renz, Thomas Unterthiner, Sepp Hochreiter, Günter Klambauer. J Chem Inf Model 2018
51
7

GuacaMol: Benchmarking Models for de Novo Molecular Design.
Nathan Brown, Marco Fiscato, Marwin H S Segler, Alain C Vaucher. J Chem Inf Model 2019
126
4


The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.
Gil Stelzer, Naomi Rosen, Inbar Plaschkes, Shahar Zimmerman, Michal Twik, Simon Fishilevich, Tsippi Iny Stein, Ron Nudel, Iris Lieder, Yaron Mazor,[...]. Curr Protoc Bioinformatics 2016
987
4

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders.
Joanna S Amberger, Carol A Bocchini, François Schiettecatte, Alan F Scott, Ada Hamosh. Nucleic Acids Res 2015
829
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.