BioinformaticsProjects

Wondering what to choose for your final year project? Here some help!!

As an undergraduate student or beginner you may find it difficult to choose your project so here are some basic ideas.

1.Structure Prediction: One take project to predict structures of proteins using various approaches like Homology Modelling, Threading and Ab-initio. Use Critical Assessment of Structure Prediction Servers 7 (CASP7) score to select the server for structure prediction. Verify these structures to select best one using SAVES server which provides Ramachandran Plot of Structure through Procheck and ERRAT2 score. Predict active site and function through motif search. Using pair-wise and multiple sequence alignment make an evolutionary relationship between proteins.Modelling of protein which has low sequence identity (less than 40%) through homology modeling is not a useful approach. Sometimes homology modeling may not predict a structure or it predicts a bad quality structure, so it’s better to use threading or ab-initio approach.
One can select such proteins which have low sequence similarity and try to predict structure which will be good for CV.
2. Developing new algorithms and Programs: If somebody is good at programming than try to develop new algorithms and programs. One can take project to develop new programs or matrices for Pair-wise or multiple alignments, for making phylogenic trees etc.

3. Search for Potential Inhibitors: If somebody is interested in drug and vaccine development than they can select projects on searching for potential inhibitors of proteins/receptors of various diseases.
One can select a particular disease and find out which proteins/receptors are expressing after disease has occurred which weren't expressing before. Try to predict their structure and search for potential inhibitors of these proteins/receptors. These inhibitors can be used as drug molecule for disease treatment using mentioned proteins/receptors as drug target.

4. Protein Function Annotation: If somebody is interested in protein function than they can select some projects on assigning functions to proteins. Protein function can be assigned by searching for the family to which protein belongs to. One can try to assign function by study of orthologus and paralogus proteins in evolutionary relationship.
Recently I had worked on some membrane proteins to predict structure, active site and mode of action using protein - substrate interaction study through docking.

Membrane proteinsare important in signal transduction. Study of these proteins is not easy because it’s hard to purify and get crystal structure of these proteins. So, one can select membrane proteins for their research projects.

DNA Binding Proteins are also very interesting topic for research project.

Source: Ravi Yadav at Quora
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