02142nas a2200265 4500008004100000022001400041245008400055210006900139260011100208300001200319490000700331520120300338653002101541653001601562653001101578653002001589100003301609700001901642700002001661700001801681700001801699700001501717700003201732856011201764 2015 eng d a1386-207300aChemoinformatics approach for building molecular networks from marine organisms0 aChemoinformatics approach for building molecular networks from m aEXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATESbBENTHAM SCIENCE PUBL LTDcJAN a673-6840 v183 a

Natural products obtained from marine sources are considered to be a rich and diverse source of potential drugs. In the present work we demonstrate the use of chemoinformatics approach for the design of new molecules inspired by molecules from marine organisms. Accordingly we have assimilated information from two major scientific domains namely chemoinformatics and biodiversity informatics to develop an interactive marine database named MIMMO (Medicinally Important Molecules from Marine Organisms). The database can be queried for species, molecules, scaffolds, drugs, diseases and associated cumulative biological activity spectrum along with links to the literature resources. Molecular informatics analysis of the molecules obtained from MIMMO was performed to study their chemical space. The distinct skeletal features of the biologically active compounds isolated from marine species were identified. Scaffold molecules and species networks were created to identify common scaffolds from marine source and drug space. An analysis of the entire molecular data revealed a unique list of around 2000 molecules from which ten most frequently occurring distinct scaffolds were obtained.

10aChemoinformatics10aDrug design10amarine10avirtual library1 aKarthikeyan, Muthukumarasamy1 aNimje, Deepika1 aPahujani, Rakhi1 aTyagi, Kushal1 aBapat, Sanket1 aVyas, Renu1 aPadmakumar, Krishna, Pillai uhttps://library.ncl.res.in/content/chemoinformatics-approach-building-molecular-networks-marine-organisms-002057nas a2200289 4500008004100000022001400041245010400055210006900159260011100228300001200339490000700351520101200358653002101370653002001391653002101411653002201432653001101454653002301465653002301488653001601511653002201527100003301549700001901582700002101601700001501622856013001637 2015 eng d a1386-207300aDesign and development of cheminfocloud: an integrated cloud enabled platform for virtual screening0 aDesign and development of cheminfocloud an integrated cloud enab aEXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATESbBENTHAM SCIENCE PUBL LTDcJAN a604-6190 v183 a

The power of cloud computing and distributed computing has been harnessed to handle vast and heterogeneous data required to be processed in any virtual screening protocol. A cloud computing platorm ChemInfoCloud was built and integrated with several chemoinformatics and bioinformatics tools. The robust engine performs the core chemoinformatics tasks of lead generation, lead optimisation and property prediction in a fast and efficient manner. It has also been provided with some of the bioinformatics functionalities including sequence alignment, active site pose prediction and protein ligand docking. Text mining, NMR chemical shift (1H, 13C) prediction and reaction fingerprint generation modules for efficient lead discovery are also implemented in this platform. We have developed an integrated problem solving cloud environment for virtual screening studies that also provides workflow management, better usability and interaction with end users using container based virtualization, OpenVz.

10aChemoinformatics10acloud computing10amachine learning10aMolecular docking10aOpenVz10asequence alignment10aspectra prediction10atext mining10avirtual screening1 aKarthikeyan, Muthukumarasamy1 aPandit, Deepak1 aBhavasar, Arvind1 aVyas, Renu uhttps://library.ncl.res.in/content/design-and-development-cheminfocloud-integrated-cloud-enabled-platform-virtual-screening-002426nas a2200241 4500008004100000022001400041245012700055210006900182260011100251300001200362490000700374520149700381653002101878653002001899653001201919653001601931653002201947100003301969700001902002700001902021700001502040856012902055 2015 eng d a1386-207300aMegaMiner: a tool for lead identification through text mining using chemoinformatics tools and cloud computing environment0 aMegaMiner a tool for lead identification through text mining usi aEXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATESbBENTHAM SCIENCE PUBL LTDcJAN a591-6030 v183 a

Virtual screening is an indispensable tool to cope with the massive amount of data being tossed by the high throughput omics technologies. With the objective of enhancing the automation capability of virtual screening process a robust portal termed MegaMiner has been built using the cloud computing platform wherein the user submits a text query and directly accesses the proposed lead molecules along with their drug-like, lead-like and docking scores. Textual chemical structural data representation is fraught with ambiguity in the absence of a global identifier. We have used a combination of statistical models, chemical dictionary and regular expression for building a disease specific dictionary. To demonstrate the effectiveness of this approach, a case study on malaria has been carried out in the present work. MegaMiner offered superior results compared to other text mining search engines, as established by F score analysis. A single query term `malaria' in the portlet led to retrieval of related PubMed records, protein classes, drug classes and 8000 scaffolds which were internally processed and filtered to suggest new molecules as potential anti-malarials. The results obtained were validated by docking the virtual molecules into relevant protein targets. It is hoped that MegaMiner will serve as an indispensable tool for not only identifying hidden relationships between various biological and chemical entities but also for building better corpus and ontologies.

10aChemoinformatics10acloud computing10amalaria10atext mining10avirtual screening1 aKarthikeyan, Muthukumarasamy1 aPandit, Yogesh1 aPandit, Deepak1 aVyas, Renu uhttps://library.ncl.res.in/content/megaminer-tool-lead-identification-through-text-mining-using-chemoinformatics-tools-and-002126nas a2200217 4500008004100000022001400041245008400055210006900139260011100208300001200319490000700331520132700338653002101665653001201686653001601698653001301714653002201727100003301749700001501782856011101797 2015 eng d a1386-207300aRole of open source tools and resources in virtual screening for drug discovery0 aRole of open source tools and resources in virtual screening for aEXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATESbBENTHAM SCIENCE PUBL LTDcJUL a528-5430 v183 a

Advancement in chemoinformatics research in parallel with availability of high performance computing platform has made handling of large scale multi-dimensional scientific data for high throughput drug discovery easier. In this study we have explored publicly available molecular databases with the help of open-source based integrated in-house molecular informatics tools for virtual screening. The virtual screening literature for past decade has been extensively investigated and thoroughly analyzed to reveal interesting patterns with respect to the drug, target, scaffold and disease space. The review also focuses on the integrated chemoinformatics tools that are capable of harvesting chemical data from textual literature information and transform them into truly computable chemical structures, identification of unique fragments and scaffolds from a class of compounds, automatic generation of focused virtual libraries, computation of molecular descriptors for structure-activity relationship studies, application of conventional filters used in lead discovery along with in-house developed exhaustive PTC (Pharmacophore, Toxicophores and Chemophores) filters and machine learning tools for the design of potential disease specific inhibitors. A case study on kinase inhibitors is provided as an example.

10aChemoinformatics10akinases10aopen source10ascaffold10avirtual screening1 aKarthikeyan, Muthukumarasamy1 aVyas, Renu uhttps://library.ncl.res.in/content/role-open-source-tools-and-resources-virtual-screening-drug-discovery-0