PRESENT LAB MEMBERS:Our email addresses are of the form "email@example.com"
PhD student, IISc
B.E. Computer Science and Engg, SSN College of Engineering-Anna University, Chennai
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.
M.Sc. Bioinformatics, Pondicherry University, Pondicherry.
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,
and folds through large-scale data analysis using high performance
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 Nnkumar
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.
Project assistant Prof. N. Srinivasan, IISc, Bangalore
M.Sc, Microbiology, Shri Bhagawan Mahavir Jain College, Bangalore.
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.
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
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 kumarreema
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.
Ph.D., Manipal University,
M.Sc., Biotechnology, Pondicherry University, Pondicherry.
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.
M.S. (Pharm) in Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hajipur (Ministry of Chemicals & Fertilizers, Dept. of Pharmaceuticals, Govt. of India).
Ph.D., Indian Institue of Science
PhD student, IISc
B.Tech (Biotech), PSG Tech-Anna University
Graduate Student with Asst.Prof Rahul Roy, Chemical Engineering IISc Bangalore
B.Tech Biotechnology,National Institute of Technology, Calicut
SHORT TERM VISITORS:
UG Student, IISc.
Int. PhD Student, Division of Biological Sciences, IISc