Kalaivani Raju | aboutI am Kalaivani Raju, a Ph.D. student in the Indian Institute of Science (IISc.), Bangalore. My area of research can be broadly described as computational biology with special focus on protein biophysics and evolution.

For my doctoral dissertation, I asked several questions on the interrelationship between the function, dynamics and structure of protein kinases. I also identified the specificity conferring residues in 107 protein kinase families, which can potentially render modularity to the kinase superfamily. I submitted my doctoral thesis on "Dynamics of protein kinases: Its relationship to functional sites and states" in January 2017 and am awaiting thesis defense shortly.

At the undergraduate level, I was trained as an engineer in Biotechnology (Anna University, Chennai, India). After the 4-year programme, I took to full-time research as a Ph.D. student in IISc. Apart from protein biology, my interests and research experiences include theoretical and cognitive neuroscience.

I am originally from Chennai, India. My current inspirations include Elon MuskKurzgesagt, Veritasium and Tim Urban.


Ph.D. in Computational Biology
Indian Institute of Science
Aug 2010 – Jan 2017

Thesis: Dyanmics of protein kinases:
Its relationship to
functional sites and states
Advisor: Prof. N. Srinivasan

B.Tech. in Industrial Biotechnology
Anna University, India
2006 – 2010

Thesis: Computational prediction of
compensatory cellular pathways
in INH-resistant M.tb.
GPA: 9.43/10.0

Tamilnadu higher secondary course
DAV M.H.S School, Tamilnadu

Biology 98.5
Maths 99.5
Physics 98.5
Chemistry 94.5

Research interests

Structural biophysics and bioinformatics

Protein evolution

Mechanistic properties of proteins
and molecular dynamics simulations

Mutated / oncogenic proteins

Design of efficient drugs

Dynamic networks of cellular signalling

Multiscale biology


Research experience

Identification of kinase-specific functional sites

Analysed 107 protein kinase families; Calculated an integrated score for every residue in each family indicative of functional specificity; Validated the identified family-specific sites in the light of relatedness, substrate-recognition and specific protein-protein interactions.

Molecular dynamics simulations of protein kinases

Simulated different functional forms of kinase catalytic domains; Characterised the differences in mobility of speicific structural motifs and scrutinised its correlation with the functional state of the kinase; Investigated the effect of bound ligand and activation loop phosphorylation on the differential mobility between kinase functional states.

Tight coupling of structural fluctuations and functions in protein kinases

Analysed the correspondence of normal mode analysis perceived structural fluctuations to the functional state of kinases; Established the conservation and conservative substitution of structural fluctuations in homologous protein kinases.

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Neuronal encoding of image segmentation in primate visual brain
Jan 2011 – Jul 2013

Carried out primate neurophysiology experiments to understand image segmentation and recognition in inferotemporal (IT) cortex; Studied various perceptual phenomena including figure-ground perception, occlusion, perception of holes and ambiguous contours.

Perceived visual blurriness as a function of spatial frequency and eccentricity using human psychophysics
Nov 2010 – Apr 2011

Varied spatial frequency and eccentricity of stimuli with respect to fovea in classical psychophysics study; Used MATLAB to quantitatively assess the psychometric function of blurriness as perceived by human subjects.

Simulation of feedback mechanisms and effects in single neuron firing
Feb 2011 – Apr 2011

Analysed different temporal patterns of feedback signal to single neurons and characterised their effects in establishing homeostatic firing rates; Used MATLAB and NEURON simulation environments.

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Prediction of circumvention of mycolic acid biosynthesis pathway in Isoniazid-resistant M.tuberculosis
Nov 2009 – Mar 2010

Used computation to postulate a feasible circumvention pathway in Isoniazid-resistant M.tuberculosis.

Quantification of gene copy numbers in strains of Pichia pastoris using real time PCR
Summer 2009

Used different molecular biology techniques for quantification of an expressed gene product; Quantified lipase B expression in various strains of Pichia pastoris using real time PCR.

Cloning and expression of recombinant lipase B in Pichia pastoris
Summer 2008

Selected strains of Pichia pastoris with high expression of cloned gene product; Cloned and expressed lipase B in fermentable concentrations.

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  1. R. Kalaivani and N. Srinivasan, A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases, Mol. BioSyst., 2015, 11, 1079-1095, DOI: 10.1039/C4MB00675E. [Download]
  2. R. Kalaivani, A. G. de Brevern and N. Srinivasan, Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites, Proteins, 2016, 84:7, 957–978, DOI: 10.1002/prot.25044 [Download]. Featured on journal cover [Download].


In preparation
  1. R. Kalaivani, R. Reema and N. Srinivasan, Recognition of sites of functional specialisation in all known eukaryotic kinases.
  2. R. Kalaivani, T. N. Narwani, A. G. de Brevern and N. Srinivasan, Microsecond-range molecular dynamics simulations of diverse forms of PKA show that the inactive forms are more dynamic than active forms.
  3. R. Kalaivani, A. G. de Brevern and N. Srinivasan, Accidental finding of a novel PKA structural conformation.
  4. R. Kalaivani and N. Srinivasan, Frequency of substitution of structural fluctuations during the evolution of protein kinases.
  5. S. Chandra, R. Kalaivani, M. Kumar, N. Srinivasan and D.P. Sarkar, Villin-induced remodelling of actin cytoskeleton enhances Sendai virus-host cell fusion.
  6. R. Reema, R. Kalaivani and N. Srinivasan, Accommodation of rogue substrates in kinase fold.

Awards and activities

EMBO travel grant

to attend workshop on modularity of signalling proteins, Seefeld in Tirol, Austria

Peer reviewer

PLOS ONE science journal

EMBO travel grant

to attend practical course on Biomolecular simulations, Pasteur Institute, Paris

Teaching assistant for undergraduate course

Neuroscience, 2nd year undergraduate course, IISc.

Senior research fellowship

Council of scientific and industrial research, India

Junior research fellowship

Council of Scientific and Industrial Research – within top 100

Silver medalist in B.Tech. Biotechnology

2nd rank among all colleges under Anna University

Graduate Aptitude test in Engineering (GATE)

All India Rank 4

Participant of CSIR Program on youth for leadership in science

One of the 50 selected participants from India

Computer skills


The following people may be contacted for reference.
Prof. N. Srinivasan | Reference
Prof. N. Srinivasan

Molecular Biophysics Unit
Indian Institute of Science
Bangalore, India
Lab webpage, Personal page


Dr. Alexandre G. de Brevern

Senior Researcher
Dr. Alexandre G. de Brevern | ReferenceFrench Institute for Health and Medical Research (INSERM)
Dynamique des Structures et Interactions des Macromolécules
Biologiques (DSIMB)
University Paris Diderot, Sorbonne Paris Cite (UP7)
National Institute for Blood Transfusion (INTS)
Paris, France
Lab webpage, Personal page


Prof. R. Sowdhamini | ReferenceProf. R. Sowdhamini

National centre for biological sciences (NCBS)
Bangalore, India
Lab webpage


Prof. N. Srinivasan's group, Lab 103, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India 560012

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