PRESENT LAB MEMBERS:

Our email addresses are of the form "user@mbu.iisc.ernet.in"


Ashraya Ravikumar

ashraya

PhD student, IISc
B.E. Computer Science and Engg, SSN College of Engineering-Anna University, Chennai
        




Gayatri Kumar

gayatrikumar

Graduate Student
M.Sc, Biotechnology, Jain University, Bangalore.
        

I am attempting to use protein like artificial sequences to bridge the gap between sequence and structural domains. Using the design strategy developed in our lab, artificial protein like sequences, intermediately relating SCOP families were generated in an attempt towards remote homology detection. In an attempt to give structural cues for sequence families without structural information I am employing designed sequences in my study. I am also, interested in studying the energy landscape of these artificial sequences and whether they adopt the fold of the parent SCOP families. Future prospects involve, exploring the unchartered fold space using both the undirected and directed sequence design approaches developed in the group.


Himani Tandon

himanit

Graduate Student,
M.Sc. Bioinformatics, Pondicherry University, Pondicherry.




Janaki Ch

janaki

Graduate Student, under External Registration Programme (ERP).
M.Sc, Genetics,Advance Diploma in Bioinformatics, Principal Technical Officer, C-DAC, Bengaluru.
        

I am working on developing computational methods for detecting remote homologues of proteins. To gain better insights into the protein structure and function, I study evolutionary relationships between protein families, superfamilies and folds through large-scale data analysis using high performance computing clusters.


Kalaivani Raju

kalaivani

PhD student
B.Tech (Biotech), Anna University
        

My work involves understanding the mechanistic basis of action and regulation in Protein Kinases, trying to bridge the structure-function gap using dynamics. I aim to achieve this using integrative dynamics approaches like Elastic Network Models, Normal Mode Analysis and Molecular Simulations, along with conventional sequence and structure methods. My studies involve establishing functional attributes to the observed dynamics and characterising the properties of unique mechanistic motions present in Protein Kinases


Kaushik H. S.

hskaushik

Graduate Student, under External Registration Programme (ERP).
M.Sc, Microbiology Bangalore University,P.G.Diploma in Bioinformatics University of Mysore.         


Short: We all love short-cuts! Well, I am evaluating worth of such shortcuts that we often take in solving structure of protein.
Long: This year 2014, is being celebrated as International Year of Crystallography. It was exactly 100 years ago the father-son duo (Bragg and Bragg) for the first time, solved structure of NaCl using X-rays. From then on, this field of crystallography has matured gracefully like red wine.

Macromolecular Crystallography has especially contributed extensively to the fields of Biochemistry, Phylogeny, Physiology, Medicine, Genetic engineering, Drug design and development to name a few. In the saga of solving structure of protein, one can either take the long route (Anomalous scattering and Isomorphous Replacement) or the short cut (Molecular Replacement). With over a million structures available in PDB database (www.rcsb.org), more often than not, we use Molecular Replacement method to solve structure of protein where a closely related structure is used to model our protein of interest. Though there are numerous sanity checks, we still don't know if this innocuous short-cut is introducing biases in the model being generated. My interest is to check if Molecular Replacement introduces any such biases. If so, which region of the protein? Is it likely to occur in loops than in helices and strands? Is it dependent on the property of amino acids? Are the biases often found on the surface of the protein than the core? Do some softwares (used in Molecular Replacement) introduce more bias than the rest? ... Most importantly, don't worry if you don't understand everything that I have mentioned above (neither do I). It's better to know few questions than all the answers!
About me: While Philosophy interests me, I am passionate about science and addicted to arts.
Caution: I am still the dumbest person I have ever known :-)


Naveen Kumar N

nkumar

Research Assistant of Dr. R. Sowdhamini, NCBS, Bangalore. Collaboration with
Prof. N. Srinivasan, IISc, Bangalore
M.Sc, (Bioinformatics),University of Madras, Chennai.

        

Understanding the functional relevance of asymmetry in heterodimeric proteins. Symmetric form often confers stability and prevalent in oligomeric proteins but mild pertubation from symmetry will be essential for dynamic functions.

Padma K

padmak

Project assistant Prof. N. Srinivasan, IISc, Bangalore
M.Sc, Microbiology, Shri Bhagawan Mahavir Jain College, Bangalore.




Prachi Mehrotra

prachim

Graduate student, IISc Mathematics Initiative
Jointly with Prof N. Chandra, Biochemistry Dept, IISc, Bangalore
B.E.(Hons) Computer Science & MSc.(Hons) Biological Science, BITS Pilani - Goa Campus.
        

The study of protein evolution and classification interests me the most. Presently my research focuses on the classification of multi-domain proteins using an alignment free approach considering the full length sequences. Alignment independent methods overcome the inherent fundamental and computational shortcomings of alignment based methods of sequence comparison.

A pattern matching alignment free method called Local Matching Score (LMS) was developed in our lab. Here, the common patterns between two sequences are scored using a substitution matrix, and scores are then normalized. It has been shown that it yields functionally relevant clusters with high domain architectural similarity. Thus using our method, we can predict the family/sub-family definition for an uncharacterized protein with high confidence.


Rakesh Ramachandran

rakesh

Graduate Student
M.Tech, Bioinformatics, University of Hyderabad, Hyderabad.
        

My current work aims to get insights into the structure of SF3b complex which is part of the Spliceosome machinery by fitting atomic-level structures of each of its individual components into the cryo-EM density map obtained at a resolution of 9.7 Å and also provide functional significance at protein-protein, protein-RNA interaction level for its components. This is being performed by taking advantage of the new homologous structures solved for the components as well as advances in both protein structure prediction techniques such as fold recognition and de novo and cryo-EM based modeling techniques such as flexible fitting. We are also using the patterns of evolutionary conservation observed at the surfaces of protein structures known to interact with other proteins as an additional restraint in our integrative structure modeling approach.

I am also part of another work on modeling of the CFTR (Cystic fibrosis transmembrane conductance regulator) protein whose structure has still not been determined by normal structure determination techniques because of its large size. The structure will be modeled using an electron crystallography map and integrative structure modeling techniques. This protein is known to contain many mutations which cause cystic fibrosis and other ailments. An independent experimental group will study the role of these mutations once the structure has been modeled. My thesis will mainly concentrate on analysis of large macromolecular assemblies and also modeling them using cryo-EM data.


Reema Anil kumar

reema

Project assistant, Prof. N. Srinivasan, IISc, Bangalore
M.Sc. Bioinformatics, Stella Maris College, Chennai.


Enzymes promote chemical reactions by bringing substrates together in an optimal orientation, contorting the substrates and creating an ideal environment. Hence enzyme - substrate reactions are highly accurate. Protein kinases regulate the majority of signal transduction pathways in cells and are important targets for the development of designer drugs. I aim at studying the physical compatibility and the extent of conservation of the same, between protein kinases and their substrates at the structural level.

Sandhya Sankaran

sandhya

Research Associate,
Ph.D., Manipal University,
M.Sc., Biotechnology, Pondicherry University, Pondicherry.


Sneha Vishwanath

snehav

Integrated PhD Student
BSc.(Hons.)Chemistry, St.Stephen's College, Delhi University
        

The questions addressed by me, revolve around modular interactions involving both protein-protein interactions as well as domain-domain interactions. The first project focused on the evolution of interface of proteases-inhibitor complexes. The second project revolves around the structural changes associated with the absence of tethered domain in multi-domain proteins.


Sohini Chakraborti

sohini

Graduate Student
M.S. (Pharm) in Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hajipur (Ministry of Chemicals & Fertilizers, Dept. of Pharmaceuticals, Govt. of India).



Srinivasan N.

ns

Head
Ph.D., Indian Institue of Science
»more


Yazhini Arangasamy

yazhinia

PhD student, IISc
B.Tech (Biotech), PSG Tech-Anna University
        









Saranaya Marimuthu

saranya

Graduate Student with Asst.Prof Rahul Roy, Chemical Engineering IISc Bangalore
B.Tech Biotechnology,National Institute of Technology, Calicut
        






SHORT TERM VISITORS:


Shamit Salim

shamitsalim@gmail.com

UG Student, IISc.

Tanzeel


Int. PhD Student, Division of Biological Sciences, IISc
        




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