A citation-based method for searching scientific literature

Alexios Koutsoukas, Robert Lowe, Yasaman Kalantarmotamedi, Hamse Y Mussa, Werner Klaffke, John B O Mitchell, Robert C Glen, Andreas Bender. J Chem Inf Model 2013
Times Cited: 95







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



Times Cited
  Times     Co-cited
Similarity


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
32

From in silico target prediction to multi-target drug design: current databases, methods and applications.
Alexios Koutsoukas, Benjamin Simms, Johannes Kirchmair, Peter J Bond, Alan V Whitmore, Steven Zimmer, Malcolm P Young, Jeremy L Jenkins, Meir Glick, Robert C Glen,[...]. J Proteomics 2011
177
32

Extended-connectivity fingerprints.
David Rogers, Mathew Hahn. J Chem Inf Model 2010
29

Relating protein pharmacology by ligand chemistry.
Michael J Keiser, Bryan L Roth, Blaine N Armbruster, Paul Ernsberger, John J Irwin, Brian K Shoichet. Nat Biotechnol 2007
27

Large-scale prediction and testing of drug activity on side-effect targets.
Eugen Lounkine, Michael J Keiser, Steven Whitebread, Dmitri Mikhailov, Jacques Hamon, Jeremy L Jenkins, Paul Lavan, Eckhard Weber, Allison K Doak, Serge Côté,[...]. Nature 2012
519
24

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
910
24

Ligand-target prediction using Winnow and naive Bayesian algorithms and the implications of overall performance statistics.
Florian Nigsch, Andreas Bender, Jeremy L Jenkins, John B O Mitchell. J Chem Inf Model 2008
69
27

Predicting new molecular targets for known drugs.
Michael J Keiser, Vincent Setola, John J Irwin, Christian Laggner, Atheir I Abbas, Sandra J Hufeisen, Niels H Jensen, Michael B Kuijer, Roberto C Matos, Thuy B Tran,[...]. Nature 2009
18

Target prediction utilising negative bioactivity data covering large chemical space.
Lewis H Mervin, Avid M Afzal, Georgios Drakakis, Richard Lewis, Ola Engkvist, Andreas Bender. J Cheminform 2015
69
26






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
947
12

How similar are similarity searching methods? A principal component analysis of molecular descriptor space.
Andreas Bender, Jeremy L Jenkins, Josef Scheiber, Sai Chetan K Sukuru, Meir Glick, John W Davies. J Chem Inf Model 2009
189
11

Gaussian interaction profile kernels for predicting drug-target interaction.
Twan van Laarhoven, Sander B Nabuurs, Elena Marchiori. Bioinformatics 2011
421
11

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
468
11

Random forest: a classification and regression tool for compound classification and QSAR modeling.
Vladimir Svetnik, Andy Liaw, Christopher Tong, J Christopher Culberson, Robert P Sheridan, Bradley P Feuston. J Chem Inf Comput Sci 2003
11

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
11

Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance.
Andreas Bender, Hamse Y Mussa, Robert C Glen, Stephan Reiling. J Chem Inf Comput Sci 2004
240
10

Molecular similarity: a key technique in molecular informatics.
Andreas Bender, Robert C Glen. Org Biomol Chem 2004
352
10

Global mapping of pharmacological space.
Gaia V Paolini, Richard H B Shapland, Willem P van Hoorn, Jonathan S Mason, Andrew L Hopkins. Nat Biotechnol 2006
550
10

DrugBank 4.0: shedding new light on drug metabolism.
Vivian Law, Craig Knox, Yannick Djoumbou, Tim Jewison, An Chi Guo, Yifeng Liu, Adam Maciejewski, David Arndt, Michael Wilson, Vanessa Neveu,[...]. Nucleic Acids Res 2014
10

ZINC: a free tool to discover chemistry for biology.
John J Irwin, Teague Sterling, Michael M Mysinger, Erin S Bolstad, Ryan G Coleman. J Chem Inf Model 2012
10




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
9

Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors.
James H Nettles, Jeremy L Jenkins, Andreas Bender, Zhan Deng, John W Davies, Meir Glick. J Med Chem 2006
124
9

Machine learning methods in chemoinformatics.
John B O Mitchell. Wiley Interdiscip Rev Comput Mol Sci 2014
177
9

Toward more realistic drug-target interaction predictions.
Tapio Pahikkala, Antti Airola, Sami Pietilä, Sushil Shakyawar, Agnieszka Szwajda, Jing Tang, Tero Aittokallio. Brief Bioinform 2015
158
9

Deep neural nets as a method for quantitative structure-activity relationships.
Junshui Ma, Robert P Sheridan, Andy Liaw, George E Dahl, Vladimir Svetnik. J Chem Inf Model 2015
371
9

Tools for in silico target fishing.
Adrià Cereto-Massagué, María José Ojeda, Cristina Valls, Miquel Mulero, Gerard Pujadas, Santiago Garcia-Vallve. Methods 2015
76
11

Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction.
Yong Liu, Min Wu, Chunyan Miao, Peilin Zhao, Xiao-Li Li. PLoS Comput Biol 2016
152
9

Diversity selection of compounds based on 'protein affinity fingerprints' improves sampling of bioactive chemical space.
Ha P Nguyen, Alexios Koutsoukas, Fazlin Mohd Fauzi, Georgios Drakakis, Mateusz Maciejewski, Robert C Glen, Andreas Bender. Chem Biol Drug Des 2013
13
61

DrugBank: a knowledgebase for drugs, drug actions and drug targets.
David S Wishart, Craig Knox, An Chi Guo, Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, Murtaza Hassanali. Nucleic Acids Res 2008
8

Chemogenomics approaches to rationalizing the mode-of-action of traditional Chinese and Ayurvedic medicines.
Fazlin Mohd Fauzi, Alexios Koutsoukas, Robert Lowe, Kalpana Joshi, Tai-Ping Fan, Robert C Glen, Andreas Bender. J Chem Inf Model 2013
34
23

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
8

PDTD: a web-accessible protein database for drug target identification.
Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang, Hualiang Jiang. BMC Bioinformatics 2008
188
8

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
8

PASS: prediction of activity spectra for biologically active substances.
A Lagunin, A Stepanchikova, D Filimonov, V Poroikov. Bioinformatics 2000
278
8

Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus laevis Phenotypic Readouts.
Sonia Liggi, Georgios Drakakis, Adam E Hendry, Kimberley M Hanson, Suzanne C Brewerton, Grant N Wheeler, Michael J Bodkin, David A Evans, Andreas Bender. Mol Inform 2013
11
72

Prediction of drug-target interactions and drug repositioning via network-based inference.
Feixiong Cheng, Chuang Liu, Jing Jiang, Weiqiang Lu, Weihua Li, Guixia Liu, Weixing Zhou, Jin Huang, Yun Tang. PLoS Comput Biol 2012
438
8

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces.
Yoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge, Wataru Honda, Minoru Kanehisa. Bioinformatics 2008
510
8

Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts.
Sonia Liggi, Georgios Drakakis, Alexios Koutsoukas, Isidro Cortes-Ciriano, Patricia Martínez-Alonso, Thérèse E Malliavin, Adrian Velazquez-Campoy, Suzanne C Brewerton, Michael J Bodkin, David A Evans,[...]. Future Med Chem 2014
16
50


QSAR modeling: where have you been? Where are you going to?
Artem Cherkasov, Eugene N Muratov, Denis Fourches, Alexandre Varnek, Igor I Baskin, Mark Cronin, John Dearden, Paola Gramatica, Yvonne C Martin, Roberto Todeschini,[...]. J Med Chem 2014
762
8

A comprehensive map of molecular drug targets.
Rita Santos, Oleg Ursu, Anna Gaulton, A Patrícia Bento, Ramesh S Donadi, Cristian G Bologa, Anneli Karlsson, Bissan Al-Lazikani, Anne Hersey, Tudor I Oprea,[...]. Nat Rev Drug Discov 2017
943
8

Predicting the mechanism of phospholipidosis.
Robert Lowe, Hamse Y Mussa, Florian Nigsch, Robert C Glen, John Bo Mitchell. J Cheminform 2012
36
19


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.