메뉴 건너뛰기




Volumn 18, Issue 6, 2015, Pages 591-603

Mega miner: A tool for lead identification through text mining using chemoinformatics tools and cloud computing environment

Author keywords

Chemoinformatics; Cloud computing; Malaria; Text mining; Virtual screening

Indexed keywords

PROTEIN; ANTIMALARIAL AGENT;

EID: 84942121292     PISSN: 13862073     EISSN: 18755402     Source Type: Journal    
DOI: 10.2174/1386207318666150703113525     Document Type: Article
Times cited : (5)

References (54)
  • 1
    • 70350776719 scopus 로고    scopus 로고
    • Malaria: A research agenda for the eradication era
    • Kilama, W.; Ntoumi, F. Malaria: A research agenda for the eradication era. Lancet, 2009, 374, 1480-1482.
    • (2009) Lancet , vol.374 , pp. 1480-1482
    • Kilama, W.1    Ntoumi, F.2
  • 4
    • 31944444061 scopus 로고    scopus 로고
    • Malaria parasite can develop stable resistance to Artemisinin but lack mutations in candidate genes atp6(Encoding the sarcoplasmic and endoplamic reticulum Ca2+ Atpase), tctp, mdr1 and cg10
    • Afonso A.; Hunt, P.; Cheeseman, H.; Alves, A.C.; Cunha C.V.; Rosario, V. do; Cravo, P. Malaria parasite can develop stable resistance to Artemisinin but lack mutations in candidate genes atp6(Encoding the sarcoplasmic and endoplamic reticulum Ca2+ Atpase), tctp, mdr1 and cg10. Antimicrob. Agents Chemother., 2008, 50(2) 480-489.
    • (2008) Antimicrob. Agents Chemother , vol.50 , Issue.2 , pp. 480-489
    • Afonso, A.1    Cunha, C.V.2    Hunt, P.3    Cheeseman, H.4    Alves, A.C.5    Do Rosario, V.6    Cravo, P.7
  • 6
    • 77954142043 scopus 로고    scopus 로고
    • Mining connections between chemicals, proteins and diseases extracted from Medline Annotations
    • Baker, N.C.; Hemminger, B.M. Mining connections between chemicals, proteins and diseases extracted from Medline Annotations. J. Biomed. Inform., 2010, 43, 510-519.
    • (2010) J. Biomed. Inform. , vol.43 , pp. 510-519
    • Baker, N.C.1    Hemminger, B.M.2
  • 7
    • 70349437274 scopus 로고    scopus 로고
    • Collaborative text annotation resource for disease centered relation extraction from biomedical text
    • Cano, C.; Monaghan, T.; Blanco, A.; Wall, D.P.; Peshkin, L. Collaborative text annotation resource for disease centered relation extraction from biomedical text. J. Biomed. Inform., 2009, 42, 966- 977.
    • (2009) J. Biomed. Inform. , vol.42 , pp. 966-977
    • Cano, C.1    Monaghan, T.2    Blanco, A.3    Wall, D.P.4    Peshkin, L.5
  • 10
    • 51049110331 scopus 로고    scopus 로고
    • Linking genes to literature: Text mining, information extraction, and retrieval applications for biology
    • Krallinger, M.; Valencia, A.; Hirschman, L. Linking genes to literature: Text mining, information extraction, and retrieval applications for biology. Genome Biol., 2008, 9 (Suppl 2), S8.
    • (2008) Genome Biol. , vol.9 , pp. S8
    • Krallinger, M.1    Valencia, A.2    Hirschman, L.3
  • 12
    • 70349437274 scopus 로고    scopus 로고
    • Collaborative text annotation resource for disease centered relation extraction from biomedical text
    • Cano, C.; Monaghan T.; Blance A.; Wall, D.P.; Peshkin L. Collaborative text annotation resource for disease centered relation extraction from biomedical text. J. Biomed. Inform., 2009, 42(5), 967-977.
    • (2009) J. Biomed. Inform. , vol.42 , Issue.5 , pp. 967-977
    • Peshkin, L.1    Cano, C.2    Monaghan, T.3    Blance, A.4    Wall, D.P.5
  • 13
    • 10244245424 scopus 로고    scopus 로고
    • BioRAT: Extracting biological information from full-length papers
    • Corney, D. P. A.; Buxton, B. F.; Langdon, W. B.; Jones, D. T. BioRAT: extracting biological information from full-length papers. Bioinformatics, 2004, 20, 3206-3213.
    • (2004) Bioinformatics , vol.20 , pp. 3206-3213
    • Corney, D.P.A.1    Buxton, B.F.2    Langdon, W.B.3    Jones, D.T.4
  • 14
    • 15844409377 scopus 로고    scopus 로고
    • MedKit: A helper toolkit for automatic mining of MEDLINE/PubMed citations
    • Ding, J.; Berleant, D. MedKit: A helper toolkit for automatic mining of MEDLINE/PubMed citations. Bioinformatics, 2005, 21, 694- 695.
    • (2005) Bioinformatics , vol.21 , pp. 694-695
    • Ding, J.1    Berleant, D.2
  • 15
    • 24144445414 scopus 로고    scopus 로고
    • Applying GIFT, a gene interactions finder in text, to fly literature
    • Domedel-Puig, N.; Wernisch, L. Applying GIFT, a gene interactions finder in text, to fly literature. Bioinformatics, 2005, 21, 3582-3583.
    • (2005) Bioinformatics , vol.21 , pp. 3582-3583
    • Domedel-Puig, N.1    Wernisch, L.2
  • 16
    • 44349084276 scopus 로고    scopus 로고
    • IDMap: Facilitating the detection of potential leads with therapeutic targets
    • Ha, S.; Seo, Y.-J.; Kwon, M.-S.; Chang, B.-H.; Han, C.-K.; Yoon, J.-H. IDMap: facilitating the detection of potential leads with therapeutic targets. Bioinformatics, 2008, 24, 1413-1415.
    • (2008) Bioinformatics , vol.24 , pp. 1413-1415
    • Ha, S.1    Seo, Y.-J.2    Kwon, M.-S.3    Chang, B.-H.4    Han, C.-K.5    Yoon, J.-H.6
  • 18
    • 33644861218 scopus 로고    scopus 로고
    • BioContrasts: Extracting and exploiting protein-protein contrastive relations from biomedical literature
    • Kim, J.-j.; Zhang, Z.; Park, J. C.; Ng, S.-K. BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature. Bioinformatics, 2006, 22, 597-605.
    • (2006) Bioinformatics , vol.22 , pp. 597-605
    • Kim, J.-J.1    Zhang, Z.2    Park, J.C.3    Ng, S.-K.4
  • 20
    • 84928096506 scopus 로고    scopus 로고
    • Cloud computing: What is it and could it be useful?
    • Andriole, K. P.; Khorasani, R. Cloud computing: what is it and could it be useful? J. Am. Coll. Radiol., 2010, 7, 252-254.
    • (2010) J. Am. Coll. Radiol. , vol.7 , pp. 252-254
    • Andriole, K.P.1    Khorasani, R.2
  • 21
    • 84859485605 scopus 로고    scopus 로고
    • Getting started with cloud computing: Offloading ancillary applications helps data center expand without adding cost or staff
    • Cantrell, D.; Maluf, M. Getting started with cloud computing: offloading ancillary applications helps data center expand without adding cost or staff. Health Manag. Technol., 2012, 33, 10-11.
    • (2012) Health Manag. Technol. , vol.33 , pp. 10-11
    • Cantrell, D.1    Maluf, M.2
  • 22
    • 78751680760 scopus 로고    scopus 로고
    • Translational bioinformatics in the cloud: An affordable alternative
    • Dudley, J. T.; Pouliot, Y.; Chen, R.; Morgan, A. A.; Butte, A. J. Translational bioinformatics in the cloud: An affordable alternative. Genome Med., 2010, 2, 51.
    • (2010) Genome Med , vol.2 , pp. 51
    • Dudley, J.T.1    Pouliot, Y.2    Chen, R.3    Morgan, A.A.4    Butte, A.J.5
  • 23
    • 79955676390 scopus 로고    scopus 로고
    • PeakRanger: A cloud-enabled peak caller for ChIP-seq data
    • Feng, X.; Grossman, R.; Stein, L. PeakRanger: A cloud-enabled peak caller for ChIP-seq data. BMC Bioinformatics, 2011, 12, 139.
    • (2011) BMC Bioinformatics , vol.12 , pp. 139
    • Feng, X.1    Grossman, R.2    Stein, L.3
  • 25
    • 84942081273 scopus 로고    scopus 로고
    • Design and development of ChemInfoCloud: An integrated Cloud enabled platform for virtual screening
    • Karthikeyan, M.; Pandit, D.; Bhavasar, A.; Vyas, R. Design and Development of ChemInfoCloud: An integrated Cloud enabled platform for virtual screening. Comb. Chem. High. Throughput Screen.,, 2015, 18(6), 604-619.
    • (2015) Comb. Chem. High. Throughput Screen , vol.18 , Issue.6 , pp. 604-619
    • Karthikeyan, M.1    Pandit, D.2    Bhavasar, A.3    Vyas, R.4
  • 26
    • 85039827039 scopus 로고    scopus 로고
    • accessed on 24th May 2014
    • http://www.sp2000.org/(accessed on 24th May 2014).
  • 27
    • 84866047935 scopus 로고    scopus 로고
    • accessed on 24th May 2014
    • LingPipe 4.1.0. http://alias-i.com/lingpipe (accessed on 24th May 2014).
    • LingPipe 4.1.0
  • 29
    • 85039815991 scopus 로고    scopus 로고
    • Accessed on 24th May 2014
    • www.chemaxon.com (Accessed on 24th May 2014).
  • 30
    • 84942134992 scopus 로고    scopus 로고
    • Scaffoldpedia unpublished results
    • Scaffoldpedia unpublished results.
  • 31
    • 84942099657 scopus 로고    scopus 로고
    • ChemScreener: A distributed computing tool for scaffold based virtual screening
    • Karthikeyan, M.; Pandit, D.; Vyas, R. ChemScreener: A distributed computing tool for scaffold based virtual screening. Comb. Chem. High Throughput Screen., 2015, 18(6), 544-561.
    • (2015) Comb. Chem. High Throughput Screen , vol.18 , Issue.6 , pp. 544-561
    • Karthikeyan, M.1    Pandit, D.2    Vyas, R.3
  • 32
    • 79953005609 scopus 로고    scopus 로고
    • PaDEL-Descriptor: An open source software to calculate molecular descriptors and fingerprints
    • Yap, C.W. PaDEL-Descriptor: An open source software to calculate molecular descriptors and fingerprints. J. Comput. Chem., 2011, 32, 1466-1474.
    • (2011) J. Comput. Chem. , vol.32 , pp. 1466-1474
    • Yap, C.W.1
  • 33
    • 33749628876 scopus 로고    scopus 로고
    • Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers
    • Monge, A.; Arrault, Al.; Marot, C.; Morin-Allory, L. Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers. Mol. Divers., 2006, 10, 389- 403.
    • (2006) Mol. Divers. , vol.10 , pp. 389-403
    • Monge, A.1    Arrault, Al.2    Marot, C.3    Morin-Allory, L.4
  • 34
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading
    • Trott, O.; Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J. Comput. Chem., 2010, 31, 455- 461.
    • (2010) J. Comput. Chem. , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 35
    • 9444225935 scopus 로고    scopus 로고
    • Java Tree view -extensible visualization of microarray data
    • Saldanha, A. Java Tree view -extensible visualization of microarray data. Bioinformatics, 2004, 20, 3246-3248.
    • (2004) Bioinformatics , vol.20 , pp. 3246-3248
    • Saldanha, A.1
  • 37
    • 84942134993 scopus 로고    scopus 로고
    • Chemical text mining for lead discovery
    • Springer
    • Karthikeyan, M; Vyas, R. Chemical text mining for lead discovery. In Practical Chemoinformatics, Springer, 2014, pp. 415-455.
    • (2014) Practical Chemoinformatics , pp. 415-455
    • Karthikeyan, M.1    Vyas, R.2
  • 38
    • 85039824730 scopus 로고    scopus 로고
    • accessed on 28 Nov 2014
    • http://java.sun.com/developer/onlineTraining/rmi/RMI.html (accessed on 28 Nov 2014).
  • 39
    • 85039829112 scopus 로고    scopus 로고
    • accessed on 24th May 2014
    • http://hadoop.apache.org/(accessed on 24th May 2014).
  • 40
    • 85039824131 scopus 로고    scopus 로고
    • accessed on 28 Nov 2014
    • http://www.cas.org/content/regulated-chemicals(accessed on 28 Nov 2014).
  • 41
    • 82055181537 scopus 로고    scopus 로고
    • In vitro culture of Plasmodium berghei maintains infectivity of mouse erythrocytes inducing cerebral malaria
    • Jambou, R.; El-Assad, F.; Combes, V.; Grau, G.E. In vitro culture of Plasmodium berghei maintains infectivity of mouse erythrocytes inducing cerebral malaria. Malar. J., 2011(10), 346.
    • (2011) Malar. J. , Issue.10 , pp. 346
    • Jambou, R.1    El-Assad, F.2    Combes, V.3    Grau, G.E.4
  • 43
    • 85039823503 scopus 로고    scopus 로고
    • accessed on 28th November 2014
    • www.coremine.com (accessed on 28th November 2014).
  • 44
    • 54949108677 scopus 로고    scopus 로고
    • PubChem: Integrated platform of small molecules and biological activities
    • Chapter 12
    • Bolton, E.E.; Wang, Y.; Thiessen, P.A.; Bryant, S.H. Chapter 12 PubChem: Integrated Platform of Small Molecules and Biological Activities. Annu. Rep. Comput. Chem., 2008, 4:217-241.
    • (2008) Annu. Rep. Comput. Chem. , vol.4 , pp. 217-241
    • Bolton, E.E.1    Wang, Y.2    Thiessen, P.A.3    Bryant, S.H.4
  • 45
    • 84942134998 scopus 로고    scopus 로고
    • North Carolina State University, Raleigh, NC and Mount Desert Island Biological Laboratory, Salisbury Cove, Maine. World Wide Web
    • Curated chemical-disease data were retrieved from the Comparative Toxicogenomics Database (CTD), North Carolina State University, Raleigh, NC and Mount Desert Island Biological Laboratory, Salisbury Cove, Maine. World Wide Web. 2014.
    • (2014) Curated Chemical-disease Data Were Retrieved from the Comparative Toxicogenomics Database (CTD)
  • 46
    • 0036084258 scopus 로고    scopus 로고
    • TTD: Therapeutic target database
    • Chen, X: TTD: Therapeutic Target Database. Nucleic Acids Res., 2002, 30, 412-415.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 412-415
    • Chen, X.1
  • 47
    • 54949111758 scopus 로고    scopus 로고
    • FACTA: A text search engine for finding associated biomedical concepts
    • Tsuruoka, Y.; Tsujii, J.; Ananiadou, S. FACTA: A text search engine for finding associated biomedical concepts. Bioinformatics, 2008, 24(21), 2559-2560.
    • (2008) Bioinformatics , vol.24 , Issue.21 , pp. 2559-2560
    • Tsuruoka, Y.1    Tsujii, J.2    Ananiadou, S.3
  • 48
    • 0036389814 scopus 로고    scopus 로고
    • Structure of the domain III of the blood stage malaria vaccine candidate Plasmodium falciparum apical membrane antigen I (AMAI)
    • Nair, M.; Hinds, M.J.; Coley, A.M.; Hodder, A.N.; Foley, M.; Anders, R.F.; Norton, R.S. Structure of the domain III of the blood stage malaria vaccine candidate Plasmodium falciparum apical membrane antigen I (AMAI). J. Mol. Biol., 2002, 322, 741-753.
    • (2002) J. Mol. Biol. , vol.322 , pp. 741-753
    • Nair, M.1    Hinds, M.J.2    Coley, A.M.3    Hodder, A.N.4    Foley, M.5    Anders, R.F.6    Norton, R.S.7
  • 49
    • 0033120029 scopus 로고    scopus 로고
    • The crystal structure of C-terminal merozoite surface protein I at 1.8 A resolution, a highly protective malaria vaccine candidate
    • Chitarra, V.; Holm, I.; Bentley, G.A.; Petres, S.; Longacre, S. The crystal structure of C-terminal merozoite surface protein I at 1.8 A resolution, a highly protective malaria vaccine candidate. Mol. Cell, 1999, 3, 457-464.
    • (1999) Mol. Cell , vol.3 , pp. 457-464
    • Chitarra, V.1    Holm, I.2    Bentley, G.A.3    Petres, S.4    Longacre, S.5
  • 50
  • 51
    • 84857711352 scopus 로고    scopus 로고
    • Structural analysis of the Plasmodium falciparum erythrocyte membrane protein I (pfEMP1) intracellular domain reveals a conserved interaction epitope
    • Mayer, C.; Slater L.; Erat, M.C.; Conrat, R.; Vakonakis, I. Structural analysis of the Plasmodium falciparum erythrocyte membrane protein I (pfEMP1) intracellular domain reveals a conserved interaction epitope. J. Biol. Chem., 2012, 287, 7182-7189.
    • (2012) J. Biol. Chem. , vol.287 , pp. 7182-7189
    • Slater, L.1    Mayer, C.2    Erat, M.C.3    Conrat, R.4    Vakonakis, I.5
  • 52
    • 37249008065 scopus 로고    scopus 로고
    • Roles for two aminopeptidases in vacuolar haemoglobin catabolism in Plasmodium falciparum
    • Dalal, S.; Klemba, M. Roles for two aminopeptidases in vacuolar haemoglobin catabolism in Plasmodium falciparum. J. Biol. Chem., 2007, 282(49), 35978-35987.
    • (2007) J. Biol. Chem. , vol.282 , Issue.49 , pp. 35978-35987
    • Dalal, S.1    Klemba, M.2
  • 53
    • 84862231099 scopus 로고    scopus 로고
    • Discovery and biochemical characterization of plasmodium thioredoxin reductase inhibotor from an anti-malarial set
    • Theobald, A.J.; Caballero, I.; Coma, I.; Colemanarejo, G.; Cid, C.; Gamo, F.J.; Hibbs, M.J.; Bass, A.L.; Thomas, D.A. Discovery and biochemical characterization of plasmodium thioredoxin reductase inhibotor from an anti-malarial set. Biochemistry, 2012, 51(23) 4764-7471.
    • (2012) Biochemistry , vol.51 , Issue.23 , pp. 4764-7471
    • Theobald, A.J.1    Caballero, I.2    Coma, I.3    Colemanarejo, G.4    Cid, C.5    Gamo, F.J.6    Hibbs, M.J.7    Bass, A.L.8    Thomas, D.A.9
  • 54
    • 84877899535 scopus 로고    scopus 로고
    • Polymorphism of the parasite lactate dehydrogenase gene from Plasmodium vivax Korean isolates
    • Shin, H.I.; Kim, J.Y.; Lee, W.J.; Sohn, Y.; Lee, S.W.; Kang, Y.J.; Lee, H.W. Polymorphism of the parasite lactate dehydrogenase gene from Plasmodium vivax Korean isolates. Malaria. J., 2013, 12(1), 166.
    • (2013) Malaria. J. , vol.12 , Issue.1 , pp. 166
    • Shin, H.I.1    Kim, J.Y.2    Lee, W.J.3    Sohn, Y.4    Lee, S.W.5    Kang, Y.J.6    Lee, H.W.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.