Literature DB >> 22589384

Bioinformatics opportunities for identification and study of medicinal plants.

Vivekanand Sharma1, Indra Neil Sarkar.   

Abstract

Plants have been used as a source of medicine since historic times and several commercially important drugs are of plant-based origin. The traditional approach towards discovery of plant-based drugs often times involves significant amount of time and expenditure. These labor-intensive approaches have struggled to keep pace with the rapid development of high-throughput technologies. In the era of high volume, high-throughput data generation across the biosciences, bioinformatics plays a crucial role. This has generally been the case in the context of drug designing and discovery. However, there has been limited attention to date to the potential application of bioinformatics approaches that can leverage plant-based knowledge. Here, we review bioinformatics studies that have contributed to medicinal plants research. In particular, we highlight areas in medicinal plant research where the application of bioinformatics methodologies may result in quicker and potentially cost-effective leads toward finding plant-based remedies.

Mesh:

Year:  2012        PMID: 22589384      PMCID: PMC3603214          DOI: 10.1093/bib/bbs021

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  105 in total

1.  KEGG: kyoto encyclopedia of genes and genomes.

Authors:  M Kanehisa; S Goto
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research.

Authors:  Farit Mochamad Afendi; Taketo Okada; Mami Yamazaki; Aki Hirai-Morita; Yukiko Nakamura; Kensuke Nakamura; Shun Ikeda; Hiroki Takahashi; Md Altaf-Ul-Amin; Latifah K Darusman; Kazuki Saito; Shigehiko Kanaya
Journal:  Plant Cell Physiol       Date:  2011-11-28       Impact factor: 4.927

3.  DNA barcodes: genes, genomics, and bioinformatics.

Authors:  W John Kress; David L Erickson
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-19       Impact factor: 11.205

4.  Metabolic fingerprinting of Cannabis sativa L., cannabinoids and terpenoids for chemotaxonomic and drug standardization purposes.

Authors:  Justin Thomas Fischedick; Arno Hazekamp; Tjalling Erkelens; Young Hae Choi; Rob Verpoorte
Journal:  Phytochemistry       Date:  2010-10-30       Impact factor: 4.072

5.  MultiCASE Expert Systems and the REACH Initiative.

Authors:  Roustem D Saiakhov; Gilles Klopman
Journal:  Toxicol Mech Methods       Date:  2008       Impact factor: 2.987

6.  Pharmacophore-driven identification of PPARγ agonists from natural sources.

Authors:  Rasmus K Petersen; Kathrine B Christensen; Andreana N Assimopoulou; Xavier Fretté; Vassilios P Papageorgiou; Karsten Kristiansen; Irene Kouskoumvekaki
Journal:  J Comput Aided Mol Des       Date:  2010-11-11       Impact factor: 3.686

7.  Development of QSAR model for immunomodulatory activity of natural coumarinolignoids.

Authors:  Dharmendra K Yadav; Abha Meena; Ankit Srivastava; D Chanda; Feroz Khan; S K Chattopadhyay
Journal:  Drug Des Devel Ther       Date:  2010-09-07       Impact factor: 4.162

8.  UniProt Knowledgebase: a hub of integrated protein data.

Authors:  Michele Magrane
Journal:  Database (Oxford)       Date:  2011-03-29       Impact factor: 3.451

9.  Integrating findings of traditional medicine with modern pharmaceutical research: the potential role of linked open data.

Authors:  Matthias Samwald; Michel Dumontier; Jun Zhao; Joanne S Luciano; Michael Scott Marshall; Kei Cheung
Journal:  Chin Med       Date:  2010-12-17       Impact factor: 5.455

10.  The Pfam protein families database.

Authors:  Marco Punta; Penny C Coggill; Ruth Y Eberhardt; Jaina Mistry; John Tate; Chris Boursnell; Ningze Pang; Kristoffer Forslund; Goran Ceric; Jody Clements; Andreas Heger; Liisa Holm; Erik L L Sonnhammer; Sean R Eddy; Alex Bateman; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2011-11-29       Impact factor: 16.971

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  15 in total

1.  Leveraging concept-based approaches to identify potential phyto-therapies.

Authors:  Vivekanand Sharma; Indra Neil Sarkar
Journal:  J Biomed Inform       Date:  2013-05-09       Impact factor: 6.317

2.  Herb Network Analysis for a Famous TCM Doctor's Prescriptions on Treatment of Rheumatoid Arthritis.

Authors:  Yan Li; Rui Li; Zibo Ouyang; Shao Li
Journal:  Evid Based Complement Alternat Med       Date:  2015-04-23       Impact factor: 2.629

3.  Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level.

Authors:  Kasper Jensen; Gianni Panagiotou; Irene Kouskoumvekaki
Journal:  PLoS Comput Biol       Date:  2014-01-16       Impact factor: 4.475

4.  Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses.

Authors:  Bhavisha P Sheth; Vrinda S Thaker
Journal:  Pharmacogn Mag       Date:  2015-10       Impact factor: 1.085

5.  Identifying Plant-Human Disease Associations in Biomedical Literature: A Case Study.

Authors:  Vivekanand Sharma; Wayne Law; Michael J Balick; Indra Neil Sarkar
Journal:  AMIA Jt Summits Transl Sci Proc       Date:  2016-07-19

6.  Antinociceptive Activity of Borreria verticillata: In vivo and In silico Studies.

Authors:  Rosa H M Silva; Nathália de Fátima M Lima; Alberto J O Lopes; Cleydlenne C Vasconcelos; José W C de Mesquita; Ludmilla S S de Mesquita; Fernando C V M Lima; Maria N de S Ribeiro; Ricardo M Ramos; Maria do Socorro de S Cartágenes; João B S Garcia
Journal:  Front Pharmacol       Date:  2017-05-22       Impact factor: 5.810

7.  Identifying Herbal Adverse Events From Spontaneous Reporting Systems Using Taxonomic Name Resolution Approach.

Authors:  Vivekanand Sharma; Luiz Fernando Fracassi Gelin; Indra Neil Sarkar
Journal:  Bioinform Biol Insights       Date:  2020-06-15

8.  Cardiovascular Disease Chemogenomics Knowledgebase-guided Target Identification and Drug Synergy Mechanism Study of an Herbal Formula.

Authors:  Hai Zhang; Shifan Ma; Zhiwei Feng; Dongyao Wang; Chengjian Li; Yan Cao; Xiaofei Chen; Aijun Liu; Zhenyu Zhu; Junping Zhang; Guoqing Zhang; Yifeng Chai; Lirong Wang; Xiang-Qun Xie
Journal:  Sci Rep       Date:  2016-09-28       Impact factor: 4.379

9.  Wu-Tou Decoction in Rheumatoid Arthritis: Integrating Network Pharmacology and In Vivo Pharmacological Evaluation.

Authors:  Qingqing Guo; Kang Zheng; Danping Fan; Yukun Zhao; Li Li; Yanqin Bian; Xuemei Qiu; Xue Liu; Ge Zhang; Chaoying Ma; Xiaojuan He; Aiping Lu
Journal:  Front Pharmacol       Date:  2017-05-03       Impact factor: 5.810

10.  In silico and in vivo characterization of cabralealactone, solasodin and salvadorin in a rat model: potential anti-inflammatory agents.

Authors:  Arif Malik; Mahwish Arooj; Tariq Tahir Butt; Sara Zahid; Fatima Zahid; Tassadaq Hussain Jafar; Sulayman Waquar; Siew Hua Gan; Sarfraz Ahmad; Muhammad Usman Mirza
Journal:  Drug Des Devel Ther       Date:  2018-05-24       Impact factor: 4.162

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