PubChem BioAssay: 2017 update

Wang, Yanli; Bryant, Stephen H.; Cheng, Tiejun; Wang, Jiyao; Gindulytė, Asta; Shoemaker, Benjamin A.; Thiessen, Paul A.; He, Siqian; Zhang, Jian

doi:10.1093/nar/gkw1118

Cited by 459 publications

(373 citation statements)

References 38 publications

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“…The phytochemical info for spices/herbs was obtained using KNApSAcK (Afendi et al, 2012) and Comparative Toxicogenomics Database (CTD) (Davis et al, 2017). All the compound identifiers were first standardized to PubChem and subsequently to MeSH in order to retrieve information regarding their bioactivity using PubChem BioAssay (Wang et al, 2017) and therapeutic associations with diseases using CTD (Davis et al, 2017).…”

Section: Methodsmentioning

confidence: 99%

SpiceRx: an integrated resource for the health impacts of culinary spices and herbs

Tuwani

Garg

et al. 2018

Preprint

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Spices and herbs are key dietary ingredients used in cuisines across the world. They have been reported to be of medicinal value for a wide variety of diseases through a large body of biomedical investigations. Bioactive phytochemicals in these plant products form the basis of their therapeutic potential as well as adverse effects. A systematic compilation of empirical data involving these aspects of culinary spices and herbs could help unravel molecular mechanisms underlying their effects on health.SpiceRx provides a platform for exploring the health impact of spices and herbs used in food preparations through a structured database of tripartite relationships with their phytochemicals and disease associations. Starting with an extensive dictionary of culinary spices and herbs, their disease associations were text mined from MEDLINE, the largest database of biomedical abstracts, assisted with manual curation. This information was further combined with spice-phytochemical and phytochemical-disease associations. SpiceRx is an integrated repertoire of evidence-based knowledge pertaining to the health impacts of culinary spices and herbs, and facilitates their disease-specific culinary recommendations as well as exploration of molecular mechanisms underlying their health effects. Availability and Implementation:SpiceRx is available at http://cosylab.iiitd.edu.in/spicerx and supports all modern browsers. SpiceRx is implemented with Python web development framework Django and relational database PostgreSQL; the front-end was built using HTML, CSS,

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Section: Methodsmentioning

confidence: 99%

SpiceRx: an integrated resource for the health impacts of culinary spices and herbs

Tuwani

Garg

et al. 2018

Preprint

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“…The computed data was analysed by using the CPPTRAJ module of AMBER-14-code. Standard angles and helicoidal parameters were determined by using algorithm adapted by Babcok et al and reference-frame-coordinate was used from Olsen et al [27][28][29]. Similarly, the helical parameters of modified-base-pairs were defined by the set of atoms of modified base-pair corresponding to the natural base-pair A-T. Nucleic acid residue names are referred to in the text as one-letter codes with a residue number; residue numbers in the 5′ to 3′ directions are represented by 1-14 for the first strand and, 15-28 for the second strand of the duplex (14-mer sequence) respectively.…”

Section: Methodsmentioning

confidence: 99%

MOLECULAR DYNAMICS STUDY OF NON-HYDROGEN-BONDING BASE-PAIR DNA DUPLEX d(GTCDNAM GCGCCGTGGC). d(GCCACGGCGCD5SICSGAC)

Tiwari

2018

Int J Pharm Pharm Sci

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Objective: The objective of the study was to elucidate the structural activity of a natural DNA sequence modified by a hydrophobic base-pair which didn't form Watson-Crick (W-C) hydrogen-bond. The modified unnatural base-pair (DNAM-D5SICS) was introduced in DNA sequences of 14-mer for molecular dynamics study in water solution. Methods:A 200 ns molecular-dynamics-simulation in orthogonal-box-water-solvent, using Particle-mesh-Ewald-method (PME) within periodicboundary-condition (PBC) was performed by using AMBER-14 code. The force-field-ff12SB-force-field was used during the simulation while the force-field-parameters of modified base-pair, compatible to ff12SB-force-field, were calculated by Gaussian-09-code using ab-inito/Hartree-Fockmethodology. The code CPPTRAJ, (a module of AMBER-14) CURVE and Chimera were used in the analysis of the data.Results: Root mean square deviation (RMSD) of heavy atoms of the trajectory revealed that the structure of the equilibrated duplex was stable, sequence-dependent and had mixed DNA-conformation. A little distortion near to the neighbor of the modified base-pair in the duplex strand was observed. However, we got a stabilized structure of such type of duplex if we placed modified base-pair after the third place in the strand. Conclusion:The study concluded that the distortion produced by modified-base-pair in the overall structure of duplex was local while the confirmation of such type of duplex was mixed and maintained the Watson-Crick (W-C) integrity of DNA. The study would help in the use of hydrophobic base-pair materials in biotechnological applications and the understanding of their structure-function relationship.

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“…PubChem BioAssay is one of PubChem sub-databases [23], [24]. It contains information regarding biological activities of small molecules.…”

Section: Rungsang Nakrumpaimentioning

confidence: 99%

“…Physical and chemical properties of a chemical molecule influence its function and activity [24], [25]. Thus chemical and physical properties of the studied chemical molecules were obtained and used as data mining attributes in this study.…”

Section: B Extracting the Physical And Chemical Propertiesmentioning

confidence: 99%

Study of Contribution of Chemical and Physical Properties of Molecules towards Their Activities against Ebola Virus Using Data Mining Techniques

R¹

2017

IJMLC

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Abstract-Ebola virus disease is a highly fatal hemorrhagic disease. To date, there is no approved drug to cure Ebola virus disease. Thus there is still the need to search for an effective drug. This study used various data mining techniques to investigate the relationship of chemical and physical properties of chemical molecules towards their activities against Ebola virus. The results suggest that these properties contribute to their activities against Ebola virus. Thus they could be used together with bioinformatics and cheminformatics techniques to help speed up the drug discovery process of Ebola virus disease.

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PubChem BioAssay: 2017 update

Cited by 459 publications

References 38 publications

SpiceRx: an integrated resource for the health impacts of culinary spices and herbs

SpiceRx: an integrated resource for the health impacts of culinary spices and herbs

MOLECULAR DYNAMICS STUDY OF NON-HYDROGEN-BONDING BASE-PAIR DNA DUPLEX d(GTCDNAM GCGCCGTGGC). d(GCCACGGCGCD5SICSGAC)

Study of Contribution of Chemical and Physical Properties of Molecules towards Their Activities against Ebola Virus Using Data Mining Techniques

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