Sandhya Sankaran

Dr. Sandhya Sankaran

Associate Professor and Head

A biologist with a deep interest in computational analysis of proteins and gene sequences. I analyze protein sequences in an evolutionary context to recognize their in-built signatures, that dictate their overall structure and function in the cellular context. Detectable relationships between proteins that harbor such signatures provide the evolutionary perspective to how proteins perform such a diverse array of functions. I am interested in using a comparative approach to decode these signatures and to understand this in the light of large milieu of interactions within a cell.


  • B.Sc. Zoology

    Stella Maris College for Women, University of Madras

  • M.Sc. Biotechnology

    Pondicherry University

  • Adv Diploma in Bioinformatics

    University of Pune

  • PhD- Bioinformatics

    Manipal University


Total Years of Experience: 23 

Academic Experience: Indian Institute of Science, National Centre for Biological Sciences –21

Industry Experience: Monsanto R&D, Astra Zeneca R&D, DSQ Biotech Ltd- 2 years

Computational Biology, Bioinformatics, Protein function, Protein evolution, Protein-protein interactions, Protein structure prediction, Molecular modelling and docking, Data analysis — All-omics platforms

National Journal Papers

  • Influence of protein structural similarities in adding value to genome data. Ind J Biotech. 2004
  • Influence of genomic and other biological data sets in the understanding of protein structures, functions and interactions. Int J Knowledge Discovery Bioinf. 2011

International Journal Papers

  • Computational tools to study RNA-protein complexes. Front Mol Biosci. 2022
  • Profiles of Natural and Designed Protein-Like Sequences Effectively Bridge Protein Sequence Gaps: Implications in Distant Homology Detection. Methods Mol Biol. 2022
  • Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex. Front Genet. 2022
  • Identification, functional characterization, assembly and structure of ToxIN type III toxin-antitoxin complex from E. coli. Nucleic Acids Res. 2022
  • Rewards of divergence in sequences, 3‑D structures and dynamics of yeast and human spliceosome SF3b complexes. Curr Res in Str Biol. 2021
  • Signatures of conserved and unique molecular features in Afrotheria. Sci Rep. 2021
  • Comparative analysis of structural and dynamical features of ribosome upon association with mRNA reveals potential role of smaller ribosomal subunit. Front Mol Biosci. 2021
  • Molecular and structural basis of cross-reactivity in M. tuberculosis toxin-antitoxin systems. Toxins. 2020
  • Artificial protein sequences enable recognition of vicinal and distant protein functional relationships. Proteins. 2020
  • Bioinformatic and mutational studies of related toxin-antitoxin pairs in M.tuberculosis predict and identify key functional residues. J Biol Chem. 2019
  • Rv0366c-Rv0367c encodes a non-canonical PezAT-like toxin-antitoxin pair. Sci Rep. 2019
  • Use of designed sequences in protein structure recognition. Biol Direct. 2018
  • Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. PLOS One. 2018
  • Protein design and its applications. Curr Opin Str Biol. 2016
  • De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. Biol Direct. 2015
  • ChExVis: A tool for molecular channel extraction and vizualization. BMC Bioinformatics. 2015
  • Bridging the islands of protein families in sequence space using artificial sequences. J Biomol Struct Dyn. 2015
  • NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. Nucleic Acids Res. 2015
  • Mapping Post-translational Modifications of Mammalian Testicular Specific Histone Variant TH2B in Tetraploid and Haploid Germ Cells and Their Implications on the Dynamics of Nucleosome Structure. J Proteome Res 2014
  • Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability. J. Mol Biol. 2014
  • Structural Annotation of the Mycobacterium tuberculosis Proteome. Microbiol Spectr. 2014
  • Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage. PLOS One. 2013
  • Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins. Mol Biosyst. 2012
  • Structural Annotation of M. tuberculosis Proteome. PLOS One. 2011
  • Influence of genomic and other biological data sets in the understanding of protein structures, functions and interactions. Int J Knowledge Discovery Bioinf. 2011
  • Length variations amongst protein domain superfamilies and consequences on structure and function. PLOS One. 2009
  • CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. BMC Struct Biol. 2008
  • Gadkari RA, Sandhya S et al, The antigen binding sites of various hCG monoclonal antibodies show homology to different domains of LH receptor. Mol Cell Endocrinol. 2007
  • Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. NAR. 2006
  • Recent trends in remote homology detection: an Indian medley. Bioinformation. 2006
  • Assessment of a rigorous transitive profile-based search method to detect remotely similar proteins. J Biomol Struct Dyn. 2005
  • Effective detection of remote homologues by searching in sequence dataset of a protein domain fold. FEBS Lett. 2003 

Books / Chapter Published

  • Relating protein families in sequence space through multiple intermediates. In Mathematical Biology, edited by P.Chandra & B.V.R.Kumar, Anamaya Publishers, New Delhi
  • Structural annotation of Mycobacterium tuberculosis proteome. Molecular Genetics of Mycobacteria, 2nd Edition, Microbiology Spectrum, ASM journals, 2014

  • 2022: Seed grant, Bioinformatics research- Ramaiah University of Applied Sciences
  • 2011 – 2014: DST post-doctoral grant in the Women Scientist scheme (WosA)
  • 2004 – 2007: CSIR award of Senior Research fellowship towards PhD
  • 1998 – 1999: DBT fellowship towards Adv. Diploma Course in Bioinformatics
  • 1998: Ranked State IV (All India XI) and in top 0.1 percentile in GATE, DoE, Govt. of India
  • UGC-NET qualification for Lectureship
  • 1996 – 1998: DBT fellowship towards M.Sc. Biotechnology, Pondicherry University, India
  • 1995- 1996: Recipient of Dr. Shiranee Pereira, Dr. Eileen Riordan, Dr. Dharmarajan awards for excellence in Zoology and Genetics-Stella Maris College for Women, University of Madras