In silico identification of disease associated with small non coding RNAs

Project Title

In silico identification of disease associated with small non coding RNAs

Project Area of Specialization Artificial IntelligenceProject Summary

The project aims to find the gene expression of diseases related to small non-coding RNA. These small non-coding RNA consists of two different categories mainly microRNA and snoRNA. These non-coding RNA are involving in the control of gene expression of all genes, our goal is to target the diseases genes and find related upregulated proteins so that these proteins can serve as drug designing basics. It will mainly include the use of different freely available online bioinformatics databases and tools. The step wise procedure to be followed is:

1. Finding the genetic disease:

The genetic disease will be searched for the purpose of study as the diseases should show up-regulated or down-regulated gene expression.

2. Finding related non-coding RNA:

Online databases will be searched to find the small non-coding RNA related to searched genetic disease. These databases are developed on the experimentally proven data.

3. Non-coding RNA and Gene expression networking:

Non-Coding RNA searched and listed using database will be analyzed for the up-regulation and down-regulation for development of disease, RNA and genes network depicting their relationship. This networking will be carried out by online tools or free available software.

4. Protein search against up-regulated genes:

Proteins against up-regulated genes or genes showing high expression will be searched for the presence of their sequences and structures. So that these proteins can be further utilized for designing drugs.

5. Protein localization and functional family prediction:

The protein will be utilized further for the localization finding and functional family prediction. Localization will be used to determine the drug type whether that will be vaccine or medicine. Functional family prediction will help to figure the ligand type easily.

6. Structure finding/Model building:

The three dimensional (3D) structure of selected protein will be searched in RCSB Protein Data Bank (PDB). If 3D structure will not be present than we will use Homology Modelling, Ab-Initio and Threading method to predict 3D model of protein.

7. Active Site prediction:

Various computational methods have been developed to explore the local secondary structures of protein and depict active site residues. One such method is Multiple Sequence Alignment (MSA) which will be used in our study along-with literature survey.

8. Docking of protein with ligands:

Protein will be docked with library of ligands to find best docked ligand using different tools such as AutoDock. Molecular Docking is a process used to find the best fitting ligand inside the active site pocket of the protein. This process helps to find the most favorable interactions between protein and ligand.

Project Objectives

The project is designed for following objectives:

1.  Better insight into disease mechanism of genetic diseases.

2. Finding of up-regulated and down-regulated genes.

3. Proteins related to upregulated genes so that they can be inhibited.

4. Docking with inhibitors.

Project Implementation Method

Protein targets will be used further for drug development against up-regulated genes. The developed drug will be utilized further for the purpose of laboratory and clinical trials.

Benefits of the Project

Following benefits will be achieved by this project:

1. The disease mechanism of non-coding RNA will be better understandable.

2. Drugs which will be harmless for human will be designed so that they can act on malfunctioned proteins affectively without causing any harm to human.

Technical Details of Final Deliverable

The protein targets: the proteins of human which are upregulated and can be used against ligand as inhibitor will be selected.

Designed drug: these drugs will be identified to be best docked ligands out of the library of ligands. These drugs can be further developed for the purpose of laboratory and clinical trials.

Final Deliverable of the Project HW/SW integrated systemType of Industry Medical Technologies OthersSustainable Development Goals Good Health and Well-Being for PeopleRequired Resources

Item Name	Type	No. of Units	Per Unit Cost (in Rs)	Total (in Rs)
			Total in (Rs)	80000
PyRx	Equipment	1	45500	45500
Simulation Fee	Equipment	3	3000	9000
Internet Facility	Equipment	10	1550	15500
Paper Rim	Miscellaneous	10	800	8000
Office Files	Miscellaneous	5	300	1500
Stationery Items	Miscellaneous	5	100	500