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
Times Cited: 1779
Times Cited
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AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.
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Oleg Trott, Arthur J Olson. J Comput Chem 2010
19
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
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
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
SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules.
Antoine Daina, Olivier Michielin, Vincent Zoete. Sci Rep 2017
Antoine Daina, Olivier Michielin, Vincent Zoete. Sci Rep 2017
13
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
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
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.
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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
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
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
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
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
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
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
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules.
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Antoine Daina, Olivier Michielin, Vincent Zoete. Nucleic Acids Res 2019
6
pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures.
Douglas E V Pires, Tom L Blundell, David B Ascher. J Med Chem 2015
Douglas E V Pires, Tom L Blundell, David B Ascher. J Med Chem 2015
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
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
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
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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.
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David Gfeller, Aurélien Grosdidier, Matthias Wirth, Antoine Daina, Olivier Michielin, Vincent Zoete. Nucleic Acids Res 2014
5
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities.
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Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N Jorissen, Michael K Gilson. Nucleic Acids Res 2007
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
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
Alexander W Schüttelkopf, Daan M F van Aalten. Acta Crystallogr D Biol Crystallogr 2004
5
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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
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5
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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
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Zhongyang Liu, Feifei Guo, Yong Wang, Chun Li, Xinlei Zhang, Honglei Li, Lihong Diao, Jiangyong Gu, Wei Wang, Dong Li,[...]. Sci Rep 2016
5
Molecular properties that influence the oral bioavailability of drug candidates.
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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.
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4
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.
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Chaolin Huang, Yeming Wang, Xingwang Li, Lili Ren, Jianping Zhao, Yi Hu, Li Zhang, Guohui Fan, Jiuyang Xu, Xiaoying Gu,[...]. Lancet 2020
4
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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
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C A Lipinski, F Lombardo, B W Dominy, P J Feeney. Adv Drug Deliv Rev 2001
4
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4
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Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
4
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4
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Daniel R Roe, Thomas E Cheatham. J Chem Theory Comput 2013
Daniel R Roe, Thomas E Cheatham. J Chem Theory Comput 2013
4
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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
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.
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4
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4
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Mariya Popova, Olexandr Isayev, Alexander Tropsha. Sci Adv 2018
4
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4
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Marcus Olivecrona, Thomas Blaschke, Ola Engkvist, Hongming Chen. J Cheminform 2017
4
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Kristina Preuer, Philipp Renz, Thomas Unterthiner, Sepp Hochreiter, Günter Klambauer. J Chem Inf Model 2018
7
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Nathan Brown, Marco Fiscato, Marwin H S Segler, Alain C Vaucher. J Chem Inf Model 2019
4
ZINC--a free database of commercially available compounds for virtual screening.
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4
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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
4
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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.