Computation Resources for Drug Discovery (CRDD)
From DrugPedia: A Wikipedia for Drug discovery
Computational Resources for Drug Discovery (CRDD) is one of the important silico modules of Open Source for Drug Discovery (OSDD). The CRDD web portal provides computer resources related to drug discovery on a single platform. Following are major features of CRDD; I) computational resources for researchers in the field of computer-aided drug design, ii) discussion form to discuss their problem with other members, iii) maintain wikipedia related to drug discovery, iv) developing database related to medicine; v) prediction of inhibitors and vi) prediction of ADMET property of molecules. One of the major objectives of CRDD is to promote open source software in the field of chemoinformatics and pharmacoinformatics. All are welcome to participate in this novel mission. Following are major features of CRDD
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Resource Compilation
Under CRDD, all the resources related to computer-aided drug designs have been collected and compiled. These resources were classify and presented on CRDD so users can got resources from single source.
Target Identification
In this category all the resources important for searching drug targets have been saved under following classes, Genome Annotation, Proteome Annotation, Potential Targets, Protein Structure
Virtual Screening
In this category all the resources important for virtual screening have been compiled under following classes, QSAR Techniques, Docking QSAR, Chemoinformatics, siRNA/miRNA
Drug Design
In this category all the resources important for designing drug inhibitors/molecules have been classify under following classes, Lead Optimization, Pharmainformatics, ADMET, Clinical Informatics
Community Contribution
Under this category platform has been developed where community may contribute in the process of drug discovery. Following are major
DrugPedia: A Wikipedia for Drug Discovery
Drugpedia is a wikipedia created for collecting and compiling information related to computer-aided drug design. The aim of Drugpedia is to provide comprehensive information about drugs. It is developed under the umbrella of Open Source Drug Discovery (OSDD) project. It covers wide range of subjects around drugs like Bioinformatics, Cheminfiormatics, clinical informatics etc
Indipedia: A wikipedia for India
Indipedia is a wikipedia created for collecting and compiling information related to India. The aim of Indipedia is to provide comprehensive information about India created for Indians by Indians. It is developed under the umbrella of Open Source Drug Discovery (OSDD) project.
CRDD Forum
CRDD Forum CRDD fourm is launch to discuss the challenge in developing computational resources for drug discovery.
Indigenous Development : Software and Web Services
Beside collecting and compiling resources, CRDD members are actively involved in developing new software and web services. All services developed are free for academic use. CRDD team is working hard to develop the Open Sources software in the field of chemoinformatics/pharmainformatics. CRDD team have dream that in coming years pubic will have platform from where they can contribute in the process of drug discovery, Following are few major tools developed at CRDD
Development of Databases
- HMRBase: It is a manually curated database of Hormones and their Receptors. It is a compilation of sequence data after extensive manual literature search and from publicly available databases. HMRbase can be searched on the basis of a variety of data types. Owing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission (Ref BMC Genomics 2009, 10:307). This database integrated in drugpedia so public can contribute.
- BIAdb: A Database for Benzylisoquinoline Alkaloids. The Benzylisoquinoline Alkaloid Database is an attempt to gather the scattered information related to the BIA's. Many BIA's show therapeutic properties and can be considered as potent drug candidates. This database will also serve researchers working in the field of synthetic biology, as developing medicinally important alkaloids using synthetic process are one of important challenges. This database integrated in drugpedia so public can contribute [Ref BMC Pharmacology 2010, 10:4
- AntigenDB: This database contain more than 500 antigens collected from literature and other immunological resources. These antigens come from 44 important pathogenic species. In AntigenDB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. AntigenDB also provides links to major internal and external databases (Ref Nucleic Acids Res. 2010: D847-53.
- PolysacDB: The PolysacDB is dedicated to provide comprehensive information about antigenic polysaccharides of microbial origin (bacterial and fungal), antibodies against them, proposed epitopes, structural detail, proposed functions, assay system, cross-reactivity related information and much more. It is a manually curated database where most of data has been collected from PubMed and PubMed Central literature databases.
Software Developed
MycoTB: In order to assist scientific community, we extended flexible system concept for building standalone software MycoTB for Windows Users. MycoTB is one of the computer program developed under OSDD/CRDD programme. This software allow user to built their own flexible system on their personal computers to mange and annotate whole proteome of MycoTB.
Resources Created
- CRAG: Computational Resources for Assembling of Genomes (CRAG) has been to assist the users in assembling of genomes from short read sequencing (SRS). Following major objective; i) Collection and compilation of computation resources, ii) Brief Description of genome assemblers, iii) Maintaing SRS and related data, iv) Service to community to assemble their genomes
- CRIP: Computational Resources for predicting protein-macromolecular interactions (CRIP) developed to provide resources related interaction. This site maintain large number of resources on interaction world of proteins that includes, protein-protein, protein-DNA, Protein-Ligand, Protein-RNA.
- BioTherapi: Bioinformatics for Therapeutic Peptides and Proteins (BioTherapi) developed for researchers working in the field of protein/peptide therapeutics. At present their is no single platform that provide this kind of information. This site include all the relevant information about the use of Peptides/Proteins in drug and synthesis of new peptides. It also cover problems, in their formulation, synthesis and delivery process
Web services for Chemoinformatics
First time in the world CRDD team has developed open source platform which allows users to predict inhibitors against novel M. Tuberculosis drug targets and other important properties of drug molecules like ADMET. Following are list of few servers.
