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BioPhytMol Help
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BioPhytMol Help & Documentation

  1. About BioPhytMol
  2. Description of Fields
  3. Simple search
  4. Query Builder
  5. Structure search
  6. Frequently Asked Questions

About:

BioPhytMol is a manually curated drug discovery resource on natural products, both plant extracts and phytomolecules that have been reported to show anti-mycobacterial properties. The data has been collected from published literature and other public resources. Currently, the resource has a total of 2582 entries that includes 188 plant families (comprised of 692 genera and 808 species) and 633 active phytomolecules identified against 25 target mycobacteria.

BioPhytMol has an extensive search tool which can be easily used to perform systematic search based on classification of the compounds to complex queries. A structure similarity tool has also been incorporated in the resource where a user can draw his/her chemical structure or load structure files (sdf, mol, mol2) that can be used to search against known anti-tuberculosis drugs, nutraceutical, FDA approved drugs and BioPhytMol phytomolecules itself. The user can perform 'substructure search', 'superstructure search' and an 'exact search'. A separate browse option has been provided for easy navigation.

Description of Fields:

The basic structure of a data unit is given below:

Field NameFull Description of Field
Compound IDA unique identifier for a particular record
Compound StructureDetailed 2D and 3D structure of the phytomolecule
Plant source and common nameInformation of the source from where the biophytmolecule was derived and its corresponding common name
Source FamilyFamily of the plant source
OriginLocation of the plant source
Plant part usedPart of the plant used for conducting experiments
ExtractInformation on prepared extract
Target bacteriaBacterial Strains against which the activity of the phytomolecule/plant extract has been checked
Assay/Test doneName of the assay used to measure the activity of the active phytomolecule identified
Positive control usedConcentration of the Reference controls used in the assay
Inhibition [%]Mycobacterial growth percent inhibition
Activity [MIC]Minimum Inhibitory Concentration value (in µg/ml)
ActivityIn terms of dilution
ActivityZone of inhibition (in mm)
Active Compound IdentifiedName of the compound identified in the plant source
PubChem IDID of the active compound identified present in PubChem database
Ethnomedicinal InformationMedicinal value of the plant source
PubMed IDID of the reference paper of PubMed database, from where the data has been extracted (if available)
Extract PreparationSteps followed for preparing the extract
Chemical ClassificationClassification assigned to the active compound identified
Media/Broth UsedInformation on the type of medium used to culture mycobacteria
Cytotoxicity AssayInformation of assay used to test cytotoxicity
Molecular WeightThe molecular weight of the active compound identified
SMILESRepresentation of the active compound identified in SMILES format
XLogPOctanol/water partition coefficient of the active compound identified
PSAPolar surface area of the active compound identified
H-bond DonorNo. of electronegative atoms in the active compound identified
H-bond AcceptorNo. of electropositive atoms in the active compound identified
No. of Rotatable Bond CountNo. of single bonds between heavy atoms in the active compound identified
No. of RingsNo. of cycles in the active compound identified
No. of NNo. of Nitrogen atoms in the active compound identified
No. of ONo. of Oxygen atoms in the active compound identified
No. of SNo. of Sulphur atoms in the active compound identified
Reference 1, 2 and 3Provides information of the reference source from where the data has been collected

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Simple search:




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Query Builder:




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Structure Similarity search:




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Frequently Asked Questions:


  1. What is BioPhytMol ?
  2. Ans. BioPhytMol is a manually curated drug discovery resource on natural products, both extracts and compounds that have been reported to show anti-mycobacterial properties. The data has been collected from published literature and other public resources.

  3. Why to search BioPhytMol?

    Ans. BioPhytMol has been developed to facilitate searching of compounds and plant extracts that have been reported to show anti-mycobacterial properties. Exploring natural product space may provide a valuable source of new, less-toxic, inexpensive, safer, accessible and reliable drugs.

  4. Can I search BioPhytMol for a molecule of interest?
  5. Ans. BioPhytMol has different search features that can be used to look for a molecule of interest. If the compound name is known, you can directly search for the compound from the homepage. If you have the SMILES, SDF, MOL or MOL2 format of the compound, you can use the BioPhytMol structure search form.

  6. How can I get the compounds/extracts having their MIC within a range?
  7. Ans.You can use the query builder. The query builder example shows how to find the compounds that have their MIC within a range.

  8. Can I find out which compounds have the least MIC?
  9. Ans.You can Browse BioPhytMol by MIC (Defined) and sort the list by the 'Activity MIC (µg/ml)' header to get the compounds with least MIC.

  10. Can I download the structure (2D/3D) of molecule of my interest?
  11. Ans. Every record in the resource (containing an active compound identified) has the option to download 2D and 3D structures in SDF and MOL format. You can find the download option just below the image of the compound.

  12. Can I search molecule having activity against particular mycobacteria?
  13. Ans. You can go to Browse by Target Bacteria page and click from a choice of 25 target mycobacteria currently available in BioPhytMol to know an active phytomolecule or plant extract and its activity against that particular mycobacteria.

  14. Can I search similar compounds from BioPhytMol using SMILES of my structure?
  15. Ans. You can use the structure search form to do such job. You can perform a substructure, superstructure and an exact structure search on BioPhytMol compounds using your SMILES. An example has been provided on the help page.

  16. Can I enter details of a new compound not available in BioPhytMol ?
  17. Ans. You can go to the submission page in order to submit data. For submission, you should be a registered sysborg member with a valid screen name and password.

  18. What can I do if I have found any error in BioPhytMol?
  19. Ans. If you find any errors in the resource, please contact any one of the team members present in the Contact us page.

  20. What messages I may report while using BioPhytMol?
  21. Ans.The below are given some messages you may report:

    Red arrow depits the instructions to be followed to make a solution.

  22. Can I get list of Mycobacterium tuberculosis (M.tb) and natural product resources from BioPhytMol?
  23. Ans. The Useful resources page in BioPhytMol website gives you the information of relevant resources on M.tb and natural products.

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