Some commonly asked questions
What is special about the annotation in this database:
We are witnessing the emergence of a web-based “data-rich” era on chemical and biological compounds. In the past decade, databases have become an integral part of research and development in the biomedical sciences. Bioinformatics now plays an essential role both in deciphering genomic, transcriptomic and proteomic data generated by high-throughput experimental technologies, as well as in organizing information gathered from traditional biology. In order to make significant advances in this “data-rich” era, it is essential to introduce techniques that allow interoperable annotation, query, and analysis across diverse data; plug-and-play scalable annotation and adoptive query tools that facilitate seamless interplay of tools and data; and versatile user interfaces that allow researchers to annotate, visualize and present the results of analysis in the most intuitive and user-friendly manner.
Databases play a major role in holding, annotating and distributing chemical, biological medicinal, and structural data (Enhanced NCI Database Browser - http://cactus.nci.nih.gov/ ; Chemistry WebBook -http://webbook.nist.gov/chemistry/ ; Thermodynamics Resource Center - http://www.trc.nist.gov; Mass Spectral Library http://www.nist.gov/srd/; Protein Data Bank - http://www.pdb.nist.gov). Such web sites are an important part of modern means of information exchange. However, the ability to organize and retrieve data remains primitive. Users need to find the most closely related information when data for a specific substance is not available, and to discover compounds with desired structural characteristics and relationships. Currently, the capability of finding similar, related substances in large, complex collections is generally unsatisfactory.
HIVSDB holds data annotated a new novel technique developed at NIST. The compounds are first indexed uniquely using IUPAC and NIST Chemical identifier (Application of INChI to curate, index and query 3-D structures; M. D. Prasanna, Jiri Vondrasek, Alexander Wlodawer, T. N. Bhat; Protein Structure, function and bioinformatics, in press 2004; INChI, http://www.iupac.org/projects/2000/2000-025-1-800.html) and organized into a data-tree such as the one shown below.
Web tools are developed to support the querying of the data using the data-tree.
How do one use the data-tree to query the database?
The data-tree may be used to query the database using several web tools. One of the web tool ( ./hiv_ligands_inhibitor_to_class.pl) allows a user to start from given type of compound such as fused rings. Then the web tools takes to the next page where all (three) fused rings are displayed ( ./hiv_ligands_class_to_subgroup.pl?T1=fused%20rings ) If one selects one of these, for instance the naphthyl group, the web tool takes to the fragment napthol ( ./hiv_ligands.pl?S1=naphthyl ). Following that the tool takes to compounds all the compounds that contain napthol fragment ( ./hiv_ligands_1.pl?name1=1-naphthol ). The tool also displays the fragments of these compounds that may be used for additional or new selection of class or subgroup or fragments. A special interface ( ./advanced_query.htm ) s provided to query the data-tree. This page allows one to perform both forward ( ./hiv_ligands_inhibitor_to_class.pl ) or reverse ( ./hiv_ligands_group_to_subgroup.pl ) query. In the forward query, one starts from a lower granularity of the data-tree and goes on to higher nodes. In the reverse mode, one starts from a compound by specifying it either from the scroll bars or using text input and then selects any one of its fragments to look for related compounds. Two types of reverse and three types of forward modes are supported at present.
How do one find all compounds with a particular fragment or fragments?
All the chemical compounds have
been annotated into standard fragments. These fragments may be chosen using the
data-tree as illustrated above (Q How do one use the data-tree to query the
database ?) or using the web tool (
./hiv_ligands.pl ) that
displays all the fragments. One may select any one of the fragments for instance
1,2-dihydropyridine and view all the compounds that have this
fragments. One may make additional choices for compounds for instance
phe and select all compounds that have both
benzaldehyde and phe. Then one may make a third
selection and obtain all the compounds that
have all these three fragments.
Can I specify multiple fragments in a single query?
Yes you may. One may specify multiple fragments in successive queries as illustrated above. Alternatively, one may also conjugate multiple fragment names or synonyms using 'AND' or 'OR'. Forr instance one may search for 'PYRROLIDINE AND 3-AMINO' groups or 'PYRROLIDINE AND DIHYDROQUINOLINE' groups by typing these strings in the text box of the URL ( ./hivsdb_fragment_search.pl ). One may use any number of OR or AND in a single query. However, both OR and AND may not be used in the same query as it results in an ambiguous query string.
How can we get additional biological data?
Query tools provide a dynamic link to the Anti-HIV Compounds Database established by NIAID using the compound IDs (View biological data).
I have a compound, I want to find compounds similar to it?
Compounds may be located either using the ID assigned in NIAID database or using their chemical name or synonyms using the tool ./hivsdb_fragment_search.pl?GQ=003504 . This will show the fragments of compound with id = 003504. One may choose any one of its fragments, for instance
and select over hundred compounds that have val. One may make further selection of fragments as explained above (how do one find all compounds with a particular fragment?)