A citation-based method for searching scientific literature

Antoine Daina, Olivier Michielin, Vincent Zoete. Nucleic Acids Res 2019
Times Cited: 537







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



Times Cited
  Times     Co-cited
Similarity


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
32

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
27


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
22

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
21

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
18

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
14

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
13


PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database.
Xia Wang, Yihang Shen, Shiwei Wang, Shiliang Li, Weilin Zhang, Xiaofeng Liu, Luhua Lai, Jianfeng Pei, Honglin Li. Nucleic Acids Res 2017
352
11

The DisGeNET knowledge platform for disease genomics: 2019 update.
Janet Piñero, Juan Manuel Ramírez-Anguita, Josep Saüch-Pitarch, Francesco Ronzano, Emilio Centeno, Ferran Sanz, Laura I Furlong. Nucleic Acids Res 2020
516
10

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
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

Shaping the interaction landscape of bioactive molecules.
David Gfeller, Olivier Michielin, Vincent Zoete. Bioinformatics 2013
151
9

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
893
9


Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment.
Runzhi Zhang, Xue Zhu, Hong Bai, Kang Ning. Front Pharmacol 2019
272
9

ETCM: an encyclopaedia of traditional Chinese medicine.
Hai-Yu Xu, Yan-Qiong Zhang, Zhen-Ming Liu, Tong Chen, Chuan-Yu Lv, Shi-Huan Tang, Xiao-Bo Zhang, Wei Zhang, Zhi-Yong Li, Rong-Rong Zhou,[...]. Nucleic Acids Res 2019
202
9


Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics.
Yunxia Wang, Song Zhang, Fengcheng Li, Ying Zhou, Ying Zhang, Zhengwen Wang, Runyuan Zhang, Jiang Zhu, Yuxiang Ren, Ying Tan,[...]. Nucleic Acids Res 2020
326
8

jvenn: an interactive Venn diagram viewer.
Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel, Christophe Klopp. BMC Bioinformatics 2014
671
8

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
7

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nucleic Acids Res 2009
7

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork,[...]. Nucleic Acids Res 2017
7



PubChem in 2021: new data content and improved web interfaces.
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 2021
520
6

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
6


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
320
6


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
443
5

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
5


The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork,[...]. Nucleic Acids Res 2021
655
5

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Damian Szklarczyk, Alberto Santos, Christian von Mering, Lars Juhl Jensen, Peer Bork, Michael Kuhn. Nucleic Acids Res 2016
544
5

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants.
Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I Furlong. Nucleic Acids Res 2017
939
5

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
5

TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models.
Zhi-Jiang Yao, Jie Dong, Yu-Jing Che, Min-Feng Zhu, Ming Wen, Ning-Ning Wang, Shan Wang, Ai-Ping Lu, Dong-Sheng Cao. J Comput Aided Mol Des 2016
99
4

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
4

HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine.
ShuangSang Fang, Lei Dong, Liu Liu, JinCheng Guo, LianHe Zhao, JiaYuan Zhang, DeChao Bu, XinKui Liu, PeiPei Huo, WanChen Cao,[...]. Nucleic Acids Res 2021
61
6

SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening.
Vincent Zoete, Antoine Daina, Christophe Bovigny, Olivier Michielin. J Chem Inf Model 2016
99
4

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses.
Zefang Tang, Chenwei Li, Boxi Kang, Ge Gao, Cheng Li, Zemin Zhang. Nucleic Acids Res 2017
4

ProTox-II: a webserver for the prediction of toxicity of chemicals.
Priyanka Banerjee, Andreas O Eckert, Anna K Schrey, Robert Preissner. Nucleic Acids Res 2018
315
4

GeneCards Version 3: the human gene integrator.
Marilyn Safran, Irina Dalah, Justin Alexander, Naomi Rosen, Tsippi Iny Stein, Michael Shmoish, Noam Nativ, Iris Bahir, Tirza Doniger, Hagit Krug,[...]. Database (Oxford) 2010
692
4

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
4

Network pharmacology.
Andrew L Hopkins. Nat Biotechnol 2007
491
4

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
4

A novel chemometric method for the prediction of human oral bioavailability.
Xue Xu, Wuxia Zhang, Chao Huang, Yan Li, Hua Yu, Yonghua Wang, Jinyou Duan, Yang Ling. Int J Mol Sci 2012
367
4

DAVID: Database for Annotation, Visualization, and Integrated Discovery.
Glynn Dennis, Brad T Sherman, Douglas A Hosack, Jun Yang, Wei Gao, H Clifford Lane, Richard A Lempicki. Genome Biol 2003
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.