1- What is PHCD?
PHCD is a free database offering information on the structures and properties of phytochemical compounds present in native Persian medicinal herbs. PHCD contains two data sets on herb and compound information. The herb information (e.g. scientific name, common name, medicinal use(s), and the lists of phytochemical ingredients found in each herb) has been manually extracted from published books and scientific journals. The compound information has been automatically calculated using various software.
2- How were the constituents of each herb determined?
Thorough literature searches were conducted to determine the constituents of each herb. The latest and more important papers were next chosen and the index of the constituents were manually extracted and organized.
3- How were the 3D structures obtained and to what extent can they be trusted?
All 3D structures were calculated at dispersion-corrected semi-empirical method PM7, using the MOPAC2016 program. The initial 3D (three-dimensional) structures of all collected compounds were either downloaded from PubChem or ChemSpider databases or were drawn and edited using GaussView0.5 or HyperChem7 programs based on the 2D structures reported in the articles reviewed.
4- How were the identifiers (i.e. SMILES, InChI, InChIKey, etc.) and pharmacophore properties (e.g. number of rotatable bonds, number of hydrogen bond acceptors and donors, logp, etc.) obtained?
All SMILESs were obtained using OpenBabel program, InChI and InChIKey strings were generated by the InChI Software, CDK fingerprints and the pharmacophore properties were produced by PaDEL software.
5- What kinds of fingerprints and similarity coefficients (or Distance Metric) have been used in the structural similarity searching?
The CDK fingerprint (1024-bit) and the Tanimoto coefficient that are currently employed for the structural similarity searching, were used here.
6- How can one leave comments or offer feedback?
All your comments and feedback are highly welcomed. You can e-mail your comments to
PHCD@ccerci.ac.ir or forward them to
Dr. Mohammad Hossein Karimi-Jafari or
Dr. Rohoullah Firouzi.
7- Can I use the information in my presentations?
Yes. You can use the 2D and 3D structures in your publications and presentations provided you cite the PHCD as instructed in the
Citing section.
8- If one cannot access the desired compound using the IUPAC nomenclature as the search entry, does it mean the compound is not indexed in PHCD?
What is the best way for finding the structures and properties of chemical compounds?
Since various IUPAC names are possible for large organic molecules, one of the following scenarios is suggested for searching the structures of chemical compounds:
A- Performing a search based on each and/or every identifier (e.g. SMILES, InChI, InChIKey) of the desired compound in the basic search bar as the fastest, most basic means for finding the compound.
B- Starting a search by drawing the 2D structure in the structure search field as your search entry, if the identifiers of the target compound are not known or available.
If none of the above strategies works, it means that your target compound is not indexed in PHCD.
9- Can I add un-indexed compounds to PHCD?
This is absolutely possible and greatly appreciated. One can do this by filling out the necessary fields in the
Data submission form or e-mailing the information together with the corresponding references through the email address provided under
Contact us and
Your comments.
10- What can I do, if I encounter an error or inconsistency in PHCD?
Please let us know about it through the links provided under Contact us menu or by Your comments. Such issues shall be certainly dealt with.
11- Do all compounds indexed in PHCD possess pharmaceutical properties?
Absolutely not! PHCD indexes the phytochemical ingredients found in Persian medicinal herbs, and not all such phytochemicals reveal pharmaceutical properties per se.
12- To what extent can the information on the medicinal effects of each herb be trusted?
All information on the medicinal effects of the herbs has been gathered from the traditional Persian medicine literatures and web resources and therefore,
PHCD does not have any resposibility on veracity thereof.
13- How can I cite the Database?
Please cite the following paper, if you are using the information from this database: