Deciphering Molecular Mechanisms in Biological Systems

We integrate biophysics, structural biology and computational biology to investigate the molecular basis of biological phenomena

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About the Lab

Led by Dr Thenmalarchelvi Rathinavelan, our lab at IIT Hyderabad focuses on the intricate world of molecular biophysics.

  • ✓ Molecular basis of repeat expansion neurodegenerative disorders by analyzing the structure and dynamics of nucleic acids and their protein complexes
  • ✓ Exploring amyloidogenic mechanism of yeast and human intrinsically disordered proteins
  • ✓ Small molecule-nucleic acid quadruplex interactions
  • ✓ Destabilization of amyloids using small molecules
  • ✓ Microbial genomics towards tackling and tracking antimicrobial resistance
  • ✓ Tracking SARS-CoV-2 evolution
  • ✓ Modeling and conformational analysis of oligosaccharides
  • ✓ Membrane protein structure and dynamics
  • ✓ Phage...bacteria interaction prediction
  • ✓ Tools and database development

Lab Members

Principal Investigator

PI

Dr Thenmalarchelvi Rathinavelan

Professor

PhD (Physics) (2005): Department of Crystallography and Biophysics, University of Madras
Mentor: Prof. N Yathinadra

Postdoc (2008): Center for Bioinformatics, University of Kansas
Advisor: Prof. Wonpil Im

Postdoc (2011): Department of Molecular Biosciences, University of Kansas
Advisor: Prof. Roberto De Guzman

Leading research in molecular biophysics with a primary focus on biomacromolecular structure, dynamics and interactions, and microbial genomics

Current Members

Ph.D. Scholars

Sruthi Sundaresan

Ph.D. Scholar

Focus: Research interests include antimicrobial resistance, structural understanding of nucleic acids, biophysical characterization of bacterial membrane proteins and the development of web tools.

Uttam Das

Ph.D. Scholar

Focus: Research focuses on the biophysical characterization of the intrinsically disordered RNA binding proteins. Main work on exploring the role of IDPs in the binding and their potential liquid-liquid phase separation (LLPS) behaviour utilizing advanced techniques like AFM, CD, and NMR.

Surabhi Srivastava

Ph.D. Scholar

Focus: Research involves the study of protein systems involved in the bacterial surface polysaccharide assembly, particularly the proteins employed in the Wzx-Wzy pathway for the translocation and adherence of capsular polysaccharides in Gram-negative bacteria.

Rohith R Kumar

Ph.D. Scholar

Focus: Research focuses on the interface of biophysics and structural biology. Interested in unravelling the interacting features of IDPs and nucleic acids.

MTech Students

Esaki Rajeswary K

Saba Farheen

Project Staff

Harsha Vardhani V

Alumni

PhD Alumni

Dr Narendar Kolimi

Asst. Professor, University of Hyderabad

Dr Yogeeshwar Ajjugal

Postdoctoral Researcher, Rutgers University, USA

Dr L Ponoop Prasad Patro

Postdoctoral Researcher, Lehigh University, USA

Dr Sathyaseelan C

Postdoctoral Researcher, University of Texas at San Antonio, USA

Dr Patil Pranita Uttamrao

Postdoctoral Fellow, IIT Bombay

MTech Alumni

Sanjana Anilkumar Nair
Ch Nimilitha
Abhishek Kumar
Bharathi Reddy Kunduru
Shivangi Sachdeva
Raghuvamsi Venkata Palur
Karpagam Uma Sudhakar
Ghule Komal Sanjeevan
Kripi Tomar
Vinothini V
Vikas Gupta
Madhusree Gangopadhyay
Janardhanaachari Roshini
Murali Aadhitya M S
Jas Chaudhary
Shivani Baskar
Akanksha Aggarwal
Sai Sindhu Manthena
Ashwath Kumar B

JRF/SRF/intern Alumni

Venkata Subbaiah
Noorain Khan
Preethi Prasanna Kamireddy
Madhu Malinee Prasad Singh
Purnima Kovuri
Sumayya Jabeen
Shivanand Rachewad

Research Interests

Molecular mechanism behind microsatellite repeat expansion disorders

Microsatellite repeat expansion disorders are a class of disorders which were discovered in 1991, in the fragile X mental retardation 1 (FMR1) gene, caused due to the expansion of a CGG repeats. Until now, nearly 40 such microsatellite repeat expansion disorders have been identified. Such an expansion results in an unusual DNA and RNA conformations and leads to several neurological and neurodegenerative disorders. There is no proper cure available for these disorders until now. To this end, our lab focuses on the unusual DNA and RNA conformations taken by such microsatellite repeat expansion disorders and their consequences in interaction with proteins. Our lab also focuses on identifying lead molecules to treat such disorders by considering DNA and RNA as the targets. We employ sub-cloning, expression, EMSA, CD, NMR and molecular dynamics simulations to address this challenging problem.

Antimicrobial resistance in Gram-negative bacteria

Multidrug resistance in Gram-negative bacteria is an important challenge the world is witnessing now. Frequent outbreak of such multidrug resistance in Gram-negative bacteria has become a health threat. In this context, using E. coli, Klebsiella spp., Acinetobacter spp. etc. as model systems we try to utilize the capsular polysaccharide (CPS or K-antigen) surface export nanomachinery as a drug target to treat these bacterial infections. Techniques employed are sub-cloning, expression, EMSA, CD, NMR and docking. Extension of this project is the in-silico serotyping of these Gram-negative bacterial species using the proteins involved in CPS surface exportation to facilitate the outbreak surveillance and disease epidemiology. Yet another extension, is modeling and creation of three-dimensional databases of CPS or K-antigen of these bacterial species.

Multi-OMICS analyses of SARS-CoV-2

Following the 2019 outbreak, our laboratory explored evolutionary tactics through pan proteomic/genomic analyses, zoonotic transmissions, and environmental monitoring to monitor viral distribution.

Amyloidogenic characteristic of an intrinsically disordered proteins

Demonstration of the ability of a Saccharomyces cerevisiae protein and its human homologue to form amyloid by employing sub-cloning, protein expression, CD, Th-T and AFM techniques. Further, understanding the mechanism of amyloid formation using mutagenesis and its consequences in human diseases.

Web Tools Development for Structural and Computational Biology

Our laboratory has developed several specialized computational tools and databases to facilitate structural biology and biophysics research. Access these tools via Tools Page.

EK3D

A curated database for Escherichia coli K-antigen three-dimensional structures

3D-NuS

A web server for automated modeling of non-canonical nucleic acid structures

K-PAM

A web-server to predict Klebsiella spp. serotypes and a database of its capsular antigens

CD-NuSS

Specialized toolto predict nucleic acid secondary structures from CD spectra using machine learning approaches

STRIDER

Tool to estimate the steric hindrance of a biomolecule/complex

ZnF-Prot

A server for proteome-wide prediction of zinc finger motifs

SSP

A web tool to predict Salmonella species serovars

ABSD

A repository of Acinetobacter baumannii K-antigen structures

CoVe-tracker

SARS-CoV-2 pan proteome evolutionary tracker

NuCDB

Circular dichroism (CD) spectral repository of nucleic acid secondary structures

MDTAP

A software to analyze permeation events across channels

3D-NuS-Qplex

A web tool to model nucleic acid quadruplexes

PaSDB

A web tool to predict Pseudomonas aeruginosa serotypes and a repository of its O-antigen 3D structures

ShigO3D

A 3-dimensional structural repository of Shigella spp. O-antigens

Global Collaborations

Molecular Dynamics Simulation

International collaboration with Dr David Fernando Estra (University of Buffalo) for Cytochrome P450 121A1 (CYP121A1) of Mycobacterium tuberculosis

Clinical surveillance of antimicrobial resistance in bacteria

Collaboration with Dr S Raja- AIIMS Bibinagar

Biomolecular NMR

Collaboration with Dr Krishna Rao (TIFR Hyderabad)

Small molecule interaction with DNA and amyloid

Collaboration with Prof G Prabu Sankar (Department of Chemistry, IITH Hyderabad)

Antimicrobial susceptibility testing of 3D-printed materials

Collaboration with Prof Subha Narayan Rath (Department of Biomedical Engineering, IITH Hyderabad)

Nucleic Acid Characterization

Collaboration with Dr Umashankar (IITGN) and Dr Umakanta (CSIR-IMMT)

Computational Tools

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Upcoming: SweetPDB

Sugar database.

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Upcoming: GlycosylDB

Glycosylation database.

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Upcoming: KPhageLink

Klebsiella-phage interaction prediction using machine learning.

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Upcoming: ShigO3D

Shigella species O-antigen repository.

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Upcoming: PaSDB

Pseudomonas aeruginosa serotyping and O-antigen repository.

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3D-NuS-Qplex

3D-Nus-Qplex is a specialized web tool designed for modeling and visualization of 3-dimensional structures of all theoretically possible nucleic acid quadruplexes.

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NuCDB

NuCDB (Nucleic acid Circular-dichroism DataBank) is a repository of nucleic acid secondary structure CD spectra published during 1964–2025, providing the sequence-structure-environmental relationship of different nucleic acid fragments on one platform, with an upload facility to keep the repository current with newly published spectra.

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MDTAP

MDTAP (Molecular Dynamics Trajectory Analysis of Permeation) is an open-source Linux/Mac-based software that automatically detects and analyzes molecular permeation events across membrane-embedded protein and nucleic acid channels from MD trajectories in DCD and PDB formats, quantifying permeation, residence time, and diffusion of solute and solvent molecules.

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ABSD

ABSD (Acinetobacter baumannii K-antigen three-dimensional Structure Database) is a 3D structural repository of 64 K-antigen monomers of the multi-drug resistant pathogen Acinetobacter baumannii, providing structural, sugar composition, and linkage information to support in silico serotyping and anti-Acinetobacter vaccine design.

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CoVe-Tracker

CoVe-Tracker (SARS-CoV-2 evolution tracker) is an interactive web-GUI database that tracks the pan-proteome evolutionary dynamics of SARS-CoV-2, providing country-wise and protein-wise amino acid mutation distributions, PANGO lineage tracking, variant evolution trends, and monthly updates based on GISAID sequences.

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SSP

SSP (Salmonella Species serotyping Predictor) is a user-friendly in silico web tool that predicts the serotypes of over 2,500 Salmonella serovars using O-antigen biosynthesis protein sequences and H-antigen filament protein sequences, achieving 99.72% prediction accuracy across 740 serovars tested on whole proteome sequences.

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ZnF-Prot

ZnF-Prot is a web server for proteome-wide prediction of zinc finger (ZnF) motifs and domains, using a combination of 74 unique sequence patterns and Pfam HMM profiles classified into 32 different ZnF classes to accurately identify ZnF domains across protein and proteome sequences of any organism.

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STRIDER

STRIDER (Steric Hindrance and Metal Coordination Identifier) is a web user interface that estimates and reports pairwise inter- and intra-molecular steric hindrances using the van der Waals radii of 117 elements, and identifies the coordination patterns of 64 metals in an interactive mode - supporting ensemble conformer analysis for flexible docking and structure-based virtual screening.

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CD-NuSS

CD-NuSS (CD to Nucleic acids Secondary Structure) is a web server that uses machine learning algorithms- XGBoost, neural network, and Kohonen- to automatically characterize the secondary structures of nucleic acids from circular dichroism spectra, trained on a curated library of 450 CD spectra spanning 16 different nucleic acid secondary structures.

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K-PAM

K-PAM (Klebsiella species serotype Predictor And surface antigens Modeler) is a unified in silico diagnostic web platform that predicts the K- and O-antigen serotypes of Klebsiella species using gene or protein sequences, hosts a 3D structural repository of modeled K- and O-antigens, and identifies hypervirulent Klebsiella pneumoniae strains.

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3D-NuS

3D-Nus (3-Dimensional Nucleic Acid Structures) is a versatile web server designed to model and visualize the 3D structures of various nucleic acid sequences, including DNA, RNA, and hybrid motifs.

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EK3D

EK3D (E. coli K antigen 3-Dimensional Structure Database) is a manually curated database of capsular polysaccharide K antigens across various E. coli serotypes, providing 3D structural models of K antigen repeating units along with sugar composition, linkage, and stereoisomeric information-facilitating antibacterial drug development against multi-drug resistant E. coli.

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Publications

2026

Untangling or further entangling? Theoretical expansion of the structural landscape of nucleic acid quadruplexes and modeling with 3D-NuS-Qplex

Rathinavelan, T. and Sundaresan, S. (2026). Briefings in Bioinformatics (In Press)

2025

An Optimized Protocol for High-Quality AFM Imaging of Amyloid Fibrils.

Kumar, R. R., Das, U., Uttamrao, P. P. and Rathinavelan, T. (2025). Bio-protocol 15(23): e5533. https://doi.org/10.21769/BioProtoc.5533

Active Site Residues Contribute to the Multistep Dynamics of Dicyclotyrosine Bound to CYP121A1 of Mycobacterium tuberculosis.

Uttamrao, P. P., Jensen, L. J., Estrada, D. F., & Rathinavelan, T. (2025). Biochemistry, 64(21), 4450–4462. https://doi.org/10.1021/acs.biochem.5c00362

Multifunctional NiO-Curcumin nanocomposite-loaded Chitosan-Alginate scaffolds for enhanced Bone Tissue Regeneration and Antibacterial Activity.

Sellappan, L. K., Mishra, S., Sundaresan, S., Rathinavelan, T., & Majumdar, S. (2025). Journal of Drug Delivery Science and Technology, 107114. https://doi.org/10.1016/j.jddst.2025.107114

MDTAP: a tool to analyze permeation events across membrane proteins.

Sruthi Sundaresan, Palur Venkata Raghuvamsi, Thenmalarchelvi Rathinavelan. Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf102. https://doi.org/10.1093/bioadv/vbaf102

2024

Computational simulation and biophysical study on cerium chloride-induced B-to-Z transition in (CG)n DNA.

Nial, P. S., Sathyaseelan, C., Bhanjadeo, M. M., Tulsiyan, K. D., Rathinavelan, T., & Subudhi, U. (2024). ACS omega, 9(47), 46784-46795. https://doi.org/10.1021/acsomega.4c04562

CHARMM at 45: Enhancements in accessibility, functionality, and speed.

Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., ... & Karplus, M. (2024). The Journal of Physical Chemistry B, 128(41), 9976-10042. https://doi.org/10.1021/acs.jpcb.4c04100

Entangled World of DNA Quadruplex Folds.

Sundaresan, S., Uttamrao, P. P., Kovuri, P., & Rathinavelan, T. (2024). ACS omega, 9(37), 38696-38709. https://doi.org/10.1021/acsomega.4c04579

G-quadruplex landscape and its regulation revealed by a new antibody capture method.

Datta, S., Patel, M., Sathyaseelan, C., Ghosh, C., Mudgal, A., Patel, D., Rathinavelan, T., & Singh, U. (2024). Oncotarget, 15, 175–198. https://doi.org/10.18632/oncotarget.28564

Asparagine-85 Stabilizes a Structural Active Site Water Network in CYP121A1 of Mycobacterium tuberculosis.

Campomizzi, C. S., Uttamrao, P. P., Stallone, J. J., Rathinavelan, T., & Estrada, D. F. (2024). Biochemistry, 63(5), 711-722. https://doi.org/10.1021/acs.biochem.3c00555

NuCDB: A databank of nucleic acids circular dichroism spectra.

Das, U., Magateshvaren Saras, M. A., & Rathinavelan, T. (2024). bioRxiv, 2024-04. https://doi.org/10.1101/2024.04.19.590190

2023

Structure and folding patterns of RNA G-quadruplexes.

Uttamrao, P. P., Sundaresan, S., & Rathinavelan, T. (2023). In RNA Structure and Function (pp. 205-232). Cham: Springer International Publishing. https://link.springer.com/chapter/10.1007/978-3-031-36390-0_10

Concentration and time-dependent amyloidogenic characteristics of intrinsically disordered N-terminal region of Saccharomyces cerevisiae Stm1.

Subbaiah SP, V., Uttamrao, P. P., Das, U., Sundaresan, S., & Rathinavelan, T. (2023). Frontiers in Microbiology, 14, 1206945. https://doi.org/10.3389/fmicb.2023.1206945

SSP: An in silico tool for Salmonella species serotyping using the sequences of O-antigen biosynthesis proteins and H-antigen filament proteins.

Sundaresan, S., & Rathinavelan, T. (2023). Journal of Molecular Biology, 435(14), 168046. https://doi.org/10.1016/j.jmb.2023.168046

Structural diversity among Acinetobacter baumannii K-antigens and its implication in the in silico serotyping.

Roshini, J., Patro, L. P. P., Sundaresan, S., & Rathinavelan, T. (2023). Frontiers in Microbiology, 14, 1191542. https://doi.org/10.3389/fmicb.2023.1191542

CoVe-tracker: an interactive SARS-CoV-2 Pan proteome evolution tracker.

Sathyaseelan, C., Magateshvaren Saras, M. A., Prasad Patro, L. P., Uttamrao, P. P., & Rathinavelan, T. (2023). Journal of Proteome Research, 22(6), 1984-1996. https://doi.org/10.1021/acs.jproteome.3c00068

Active site aromatic residues play a dual role in the substrate interaction and protein structure in functional dimers of CYP121A1 of Mycobacterium tuberculosis.

Campomizzi, C. S., Kumar, A., Uttamrao, P. P., Stallone, J. J., Ghanatios, G. E., Rathinavelan, T., & Estrada, D. F. (2023). ACS Infectious Diseases, 9(4), 827-839. https://doi.org/10.1021/acsinfecdis.2c00531

Sequence patterns and HMM profiles to predict proteome wide zinc finger motifs.

Sathyaseelan, C., Patro, L. P. P., & Rathinavelan, T. (2023). Pattern Recognition, 135, 109134. https://doi.org/10.1016/j.patcog.2022.109134

2022

SARS-CoV-2 whole-proteome sequences from environment as an indicator of community viral distribution, evolution and epidemiological dynamics: A cohort analysis of Austria.

Murali Aadhitya, MS, Patro, LPP*, Uttamrao, PP* and Rathinavelan, T. (2022). Environmental Microbiology Reports (Accepted).

Geographical distribution of SARS-CoV-2 amino acids mutations and the concomitant evolution of seven distinct clades in non-human hosts.

Murali Aadhitya, MS, Patro, LPP*, Uttamrao, PP* and Rathinavelan, T. (2022). Zoonoses and Public Health. https://doi.org/10.1111/zph.12971

STRIDER: Steric hindrance and metal coordination identifier.

Patro, LPP and Rathinavelan, T. (2022). Comput Biol Chem. https://doi.org/10.1016/j.compbiolchem.2022.107686

2021

Conformational distortions induced by periodically recurring A...A in d(CAG).d(CAG) provide stereochemical rationale for the trapping of MSH2.MSH3 in polyQ disorders.

Ajjugal, Y. and Rathinavelan, T. (2021). Comput Struct Biotechnol J. https://doi.org/10.1016/j.csbj.2021.07.018

Revelation of potent epitopes present in unannotated ORF antigens of SARS-CoV-2 using immunoinformatics approach for the polyvalent epitope vaccine design.

P. P. Uttamrao, C. Sathyaseelan*, L. P. P. Patro*, T. Rathinavelan (2021). Frontiers in Immunology. https://doi.org/10.3389/fimmu.2021.692937

Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades.

Patro, L.P.P.*, Sathyaseelan, C.*, Uttamrao, P.P.* and Rathinavelan, T. (2021). Infection, Genetics and Evolution. https://doi.org/10.1016/j.meegid.2021.104973

The evolving proteome of SARS-CoV-2 predominantly uses mutation combination strategy for survival.

Patro, L.P.P.*, Sathyaseelan, C.*, Uttamrao, P.P.* and Rathinavelan, T. (2021). Comput Struct Biotechnol J. https://doi.org/10.1016/j.csbj.2021.05.054

CD-NuSS: A Web Server for the Automated Secondary Structural Characterization of the Nucleic Acids from Circular Dichroism Spectra Using Extreme Gradient Boosting Decision-Tree, Neural Network and Kohonen Algorithms.

Sathyaseelan, C.*, Vijayakumar, V.* and Rathinavelan, T. (2021). J Mol Biol., 433(11):166629. https://doi.org/10.1016/j.jmb.2020.08.014

Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS.

Ajjugal, Y.*, Kolimi, N.* and Rathinavelan, T. (2021). Sci Rep., 11(1):8163. https://doi.org/10.1038/s41598-021-87097-y

Sequence dependent influence of an A… A mismatch in a DNA duplex: An insight into the recognition by hZαADAR1 protein.

Ajjugal, Y.*, and Rathinavelan, T. (2021). J Struct Biol., 213(1):107678. https://doi.org/10.1016/j.jsb.2020.107678

Spontaneous and frequent conformational dynamics induced by A… A mismatch in d(CAA)·d(TAG) duplex.

Ajjugal, Y.*, Tomar, K.* Rao, D.K., and Rathinavelan, T. (2021). Sci Rep., 11(1):3689. https://doi.org/10.1038/s41598-021-82669-4

2020

K-PAM: A unified platform to distinguish Klebsiella species K-and O-antigen types, model antigen structures and identify hypervirulent strains.

Patro, L.P.P.*, Sudhakar, K.U.* and Rathinavelan, T. (2020). Sci Rep., 7;10(1):16732. https://doi.org/10.1038/s41598-020-73360-1

STRIDER: Steric hindrance estimator.

Patro, L.P.P., and Rathinavelan, T. (2020). BioRxiv., 2020.02.07.931550. https://doi.org/10.1101/2020.02.07.931550

2019

Targeting the sugary armor of klebsiella species.

Patro, L.P.P., and Rathinavelan, T. (2019). Front Cell Infect Microbiol., 8,9-367. https://doi.org/10.3389/fcimb.2019.00367

2017

3D-NuS: A Web Server for Automated Modeling and Visualization of non-canonical 3-Dimensional Nucleic Acid Structures.

Patro, L.P.P.*, Kumar, A.*, Kolimi, N.* and Rathinavelan, T. (2017). J Mol Biol., 429, 2438-2448. https://doi.org/10.1016/j.jmb.2017.06.013

A B-Z junction induced by an A… A mismatch in GAC repeats in the gene for cartilage oligomeric matrix protein promotes binding with the hZαADAR1 protein.

Kolimi, N.*, Ajjugal. Y* and Rathinavelan, T. (2017). J Biol Chem. 292, 18732-18746. https://doi.org/10.1074/jbc.M117.796235

E. coli group I capsular polysaccharide exportation nanomachinary as an antivirulent target in the perspective of emerging antimicrobial resistance.

Sachdeva, S.*, Palur, R.V.*, Sudhakar, K.U.* and Rathinavelan, T. (2017). Front Microbiol 8:70. https://doi.org/10.3389/fmicb.2017.00070

2016

Selective Preference of Parallel DNA Triplexes is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity Between the G*GC and T*AT triplets.

Goldsmith, G., Rathinavelan, T. and Yathindra N. (2016). PLoS One 11(3), e0152102. https://doi.org/10.1371/journal.pone.0152102

Key Diffusion Mechanisms Involved in Water Conduction of Wzi.

Sachdeva, S.*, Kolimi, N.*, Nair, S.A.* and Rathinavelan, T. (2016). Sci. Rep. 28157. https://doi.org/10.1038/srep28157

EK3D: an E. coli K antigen 3-Dimensional Structure Database.

Kunduru, B.R.*, Nair, S.N.* and Rathinavelan, T. (2016). Nucleic Acids Res. 44 (D1), D675-D681. https://doi.org/10.1093/nar/gkv1313

2015

Twisting Right To Left: A…A Mismatch In A CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation.

Khan, N.*, Kolimi, N* and Rathinavelan, T.* (2015). PLoS Comput. Biol. https://doi.org/10.1371/journal.pcbi.1004162

From UM, IBAB & KU

2014

NMR Model of PrgI-SipD Interaction and its Implications in the Needle-Tip Assembly of the Salmonella Type III Secretion System.

Rathinavelan, T., Lara-Tejero, M., Lefebre, M., Chatterjee, S., McShan, A.C., Guo, D-C., Tang, C., Galan, J.E. and De Guzman, R.N. (2014). J. Mol. Biol. 426, 2958-69. https://doi.org/10.1016/j.jmb.2014.06.009

2011

Characterization of the Interaction between the Salmonella Type III Secretion System Tip Protein SipD and the Needle Protein PrgI by Paramagnetic Relaxation Enhancement.

Rathinavelan, T., Tang, C. and De Guzman, R.N. (2011). J. Biol. Chem. 286, 4922-30. https://doi.org/10.1074/jbc.M110.159434

2010

NMR Characterization of Hydrophobic Collapses in Amyloidogenic Partially Folded States and Their Implications for Protein Misfolding and Amyloid Formation.

Lim, K.H., Nagchowdhuri P., Rathinavelan, T. and W. Im (2010). Biochem. Biophys. Res. Commun. 396, 800-05. https://doi.org/10.1016/j.bbrc.2010.04.137

A Repulsive Electrostatic Mechanism for Protein Export through the Type III Secretion Apparatus.

Rathinavelan, T., Zhang, L., Picking, W.L., Weis, D.D., De Guzman, R.N. and Im, W. (2010). Biophy. J. 98, 452-61. (Cover page article, Highlighted paper.) https://doi.org/10.1016/j.bpj.2009.10.030

2008

A Novel Strategy to Determine Protein Structures using Exclusively Residual Dipolar Coupling.

Rathinavelan, T. and Im, W. (2008). J. Comput. Chem. 29, 1640-49. https://doi.org/10.1002/jcc.20923

2007

Differences in the Electrostatic Surfaces of the Type III Secretion Needle Proteins.

Wang, Y., Ouellette, A.N., Egan, C.W., Rathinavelan, T., Im, W. and De Guzman, R.N. (2007). J. Mol. Biol., 371, 1304-14. https://doi.org/10.1016/j.jmb.2007.06.034

Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination.

Rathinavelan, T. and Im, W. (2007). J. Comput. Chem., 28, 1858-64. https://doi.org/10.1002/jcc.20712

2006

Base triplet nonisomorphism strongly influences DNA triplex conformation: effect of nonisomorphic G*GC and A*AT triplets and bending of DNA triplexes.

Rathinavelan, T. and Yathindra, N. (2006). Biopolymers, 82, 443-61. https://doi.org/10.1002/bip.20484

2005

Molecular dynamics structures of peptide nucleic acid x DNA hybrid in the wild-type and mutated alleles of Ki-ras proto-oncogene: Stereochemical rationale for the low affinity of PNA in the presence of an A.C mismatch.

Rathinavelan, T. and Yathindra, N. (2005). FEBS J., 272, 4055-70. https://doi.org/10.1111/j.1742-4658.2005.04817.x

New insights into DNA triplexes: Residual twist and radial difference as measures of base triplet non-isomorphism and its implication to sequence dependent non-uniform DNA triplex.

Thenmalarchelvi, R. and Yathindra, N. (2005). Nucleic Acids Res., 35, 43-55. https://doi.org/10.1093/nar/gki143

2001

Targeting neighbouring poly(purine.pyrimidine) sequences located in the human bcr promoter by triplex-forming oligonucleotides.

Xodo, L.E, Rathinavelan, T., Quadrifoglio, F., Manzini, G., and Yathindra, N. (2001). Eur. J. Biochem., 268, 656-64. https://doi.org/10.1046/j.1432-1327.2001.01919.x

Book Chapters

A computational approach to explore protein translocation through type III secretion apparatus.

Rathinavelan, T. and Im, W. (2010). In Quantum Bio-Informatics: From Quantum Information to Bio-Informatics, Eds. L. Accardi, W. Freudenberg, and M. Ohya 26, 453-63.

“Residual” Hoogsteen twist as a measure of nonisomorphism in DNA base triplets: Implications to sequence dependent DNA triplexes.

Thenmalarchelvi, R. and Yathindra, N. (2003). Recent Trends in Biophysical Research, Eds. Maiti, M., Suresh Kumar, G. and Das, S., 17-24, Publishers: Double A Work Station, Kolkata, India.

Funding & Support

ANRF

Anusandhan National Research Foundation

DBT

Department of Biotechnology

BIRAC-SRISTI

Biotechnology Industry Research Assistance Council-Society for Research and Initiatives for Sustainable Technologies and Institutions

Teaching

MTech Medical Biotechnology & PhD Biotechnology

Fall Semester

Structural Bioinformatics

BT6113

Elective
Spring Semester

Biomolecular NMR

BT7053

Elective
- OR -

Programming for Biomacromolecular Data Analysis

BT6083

Elective

BTech Biotechnology and Bioinformatics

Spring Semester

Basic Bioinformatics

BT1020

Core

Events

2026

May 2026

Lab Lunch @NH65 Restaurant

Farewell party for Ashwath and Harsha. All the best.

March 27, 2026

Welcome back to India Dr Narendar

Narendar, our alumnus, gave a talk after joining as an Assistant Professor at HCU. All the Best!

March 6, 2026

Invited Talk by Dr Subha

Talk by Dr Subha from IBAB on "Extracting Unique Insights from Assembled Genomes: from nutritional plant to cancer to malaria vector to individual human genome".

Before 2026

December 30, 2025

Group Dinner @ Globe Buffetio

Welcoming the New year 2026.

August 29, 2025

RU-IITH Conference 2025

Rohith and Uttam's Poster Presentation as well as Lab visit by students and faculty from Ritsumeikan University during the RU-IITH Conference.

July 2025

Convocation of Dr. Pranita Patil

Congratulations to Dr. Pranita Patil for her PhD Convocation!

August 2025

PhD Completion – Dr. Pranita Patil

Congratulations to Dr. Pranita Patil for successfully completing her PhD!

February 28, 2025

HSCB Conference 2025

HSCB Conference conducted successfully in 2025.

February 27, 2025

Dinner with Prof. Wonpil, University of Le High, USA @ 63 Degrees Modern Region Buffet.

Prof Wonpil, one of the postdoctoral adivsors of Thenmalar visited IITH for HSCB-2025 conference.

February 15, 2025

BPS Conference 2025, USA – Sruthi Sundaresan

Sruthi Sundaresan attended the Biophysical Society (BPS) Conference in Los Angeles, USA.

December 24, 2024

Sometimes ... fun is needed

Happy moments after Pranta's OC.

December 14, 2024

Biophysics Deccan Meet 2024 @BITS Hyderabad

Thenmalar, Sruthi and Uttam attended "Biophysics Deccan Meet 2024" at BITS-Pilani, Hyderabad Campus.

September, 2024

Have a break, have some coffee

Coffee and snacks time at CCD, B Block.

February 2024

Biophysical Society Conference 2024, Philadelphia

Sruthi and Pranita attended the Biophysical Society Conference 2024 in Philadelphia, USA.

January 6, 2024

Lunch at GlobeGrub

Lab lunch get-together at GlobeGrub.

November 18, 2023

BT Foundation Day 2023 "Bio-Vridhi '23"

As a part of Bio-Vridhi '23 celebration, Sruthi, Pranita and Shivani represented our lab by participating on student talk and poster presentation.

July 15, 2023

PhD Completion – Dr. Sathyaseelan

Congratulations to Dr. Sathyaseelan on successfully completing his PhD!

July 14, 2023

Get Together at Barbeque Nation

Lab get-together and celebration at Barbeque Nation.

November 12, 2022

Department Day Poster Presentation at IITH

Poster Presentation by Sruthi and Sathyaseelan on Department Day at IIT Hyderabad.

October 20, 2022

Team Lunch at Paradise

Lab team lunch outing at Paradise.

July 14, 2023

PhD Completion – Dr. Ponoop

Congratulations to Ponoop on successfully completing his PhD and Aadhitya for his M. Tech.

April 9, 2022

Research Excellence Award – Ponoop

Ponoop received the Research Excellence Award for the year 2021.

April 3, 2022

First Post-Corona Group Lunch

Our first Post-Corona group lunch at Jonathans Kitchen 2.0 - a joyful reunion after a long time!

December 19, 2021

Farewell to Yogeesh & Lab Lunch

Farewell to Yogeesh and a lab lunch at the Academics rooftop to celebrate his journey ahead.

December 1, 2021

Pooja for New BT-BME Building at IITH

Pooja ceremony held for the new BT-BME Building at IIT Hyderabad - a major milestone for the department.

November 27, 2021

Gold Medals for Sruthi Sundaresan

Congratulations to Sruthi Sundaresan for winning athletic gold medals in Shotput and Discus - a first-of-a-kind achievement for our lab!

November 8, 2021

First Visit to Permanent Lab in BT Building

An exciting milestone - the first visit to our permanent lab space in the new BT Building at IITH.

June 30, 2021

PhD Completion – Dr. Yogeeshwar Ajjugal

Congratulations to Dr. Yogeeshwar Ajjugal on successfully completing his PhD!

June 22, 2021

Research Excellence Award – Sathyaseelan

Sathyaseelan received the Research Excellence Award (PhD Scholars 2021) from IIT Hyderabad.

October 19, 2019

Lab Visit and Lunch with Narendar

Lunch with Narendar during his lab visit.

September 25–27, 2019

International Conference on FMR1 Premutation – Netherlands

Yogeeshwar delivered an oral presentation at the 4th International Conference on FMR1 Premutation held in the Netherlands.

July 6, 2019

BIRAC SITARE GYTI Award 2019

Yogeeshwar and Narendar received the BIRAC SITARE GYTI Award 2019.

June 20, 2019

Group Outing at Exotica

Our group outing at Exotica - a fun day out together!

November 2018

Farewell to Narendar – Postdoc at Clemson

Congratulations to Narendar for securing a Postdoctoral position at Clemson University. Farewell celebrated at RedLa.

June 27, 2018

Lab Party at CCD – Hosted by Narendar

Narendar threw a party for the lab at CCD.

June 23, 2018

Group Outing – Mustang and Cream Stone

Our group outing at Mustang followed by desserts at Cream Stone.

May 28, 2018

PhD Completion – Dr. Narendar

Congratulations to Dr. Narendar on successfully defending his PhD!

April 14, 2018

Dr. KV Rao Research Award – Yogeeshwar

Yogeeshwar received the Dr. KV Rao Research Award (1st Runner Up), presented by Prof. Anurag Kumar, Director, IISc Bangalore.

March 19, 2018

GYTI-SHRISTI Appreciation Award

Ponoop, Abhishek, and Narendar received the GYTI-SHRISTI Appreciation Award, presented by Science and Technology Minister Dr. Harsh Vardhan.

February 28, 2018

National Science Day In-House Symposium 2018

On National Science Day, an in-house symposium was held - "We are always a Happy Group without Thenmalar."

July 13–15, 2017

Workshop: Essential Programming for Life Scientists

Workshop on "Essential Programming for Life Scientists" held over three days.

July 5, 2017

Group Lunch at Barbeque Nation

Our group lunch at Barbeque Nation.

May 27, 2017

Dr. KV Rao Research Award – Narendar

Narendar received the Dr. KV Rao Research Award (1st Runner Up), presented by Prof. Appa Rao, Vice-Chancellor, HCU.

March 23–25, 2017

Annual Meeting of the Indian Biophysical Society – IISER Mohali

Lab members attended the Annual Meeting of the Indian Biophysical Society at IISER Mohali.

March 5, 2017

GYTI-SHRISTI Award – Shivangi & Narendar

Shivangi and Narendar received the GYTI-SHRISTI Award.

October 10, 2016

Media Coverage – The Hindu, Science & Technology

Our research received media coverage in The Hindu, Science & Technology section.

July 3, 2016

Farewell to Shivangi

Shivangi's treat at Pine & Dine, followed by her farewell celebration at Cream Stone.

June 4, 2016

Group Dinner at Chef's Garden

Lab group dinner at Chef's Garden.

March 19, 2016

1st Workshop: Multiscale Modeling of Biomacromolecules

Our first workshop on Multiscale Modeling of Biomacromolecules.

February 8–10, 2016

Annual Meeting of the Indian Biophysical Society – IISc, Bengaluru

Lab members attended the Annual Meeting of the Indian Biophysical Society at IISc, Bengaluru.

April 12–13, 2015

Best Poster Award – Yogeeshwar & Nimilitha

Congratulations to Yogeeshwar and Nimilitha for winning the "Best Poster Award" at the International Congress on DNA Structure in Health & Disease.

April 12, 2015

Group Outing to AB's Barbecue

Lab group outing to AB's Barbecue.

March 25, 2015

Excellence in Teaching Award – Thenmalar

Thenmalar received the "Excellence in Teaching Award" for the year 2014–15.

February 7, 2015

Annual Meeting of the Indian Biophysical Society 2015

Oral presentations by Narendar and Sanjana, and a poster presentation by Bharathi at the Annual Meeting of the Indian Biophysical Society.

August 7, 2014

MTech Graduation – Nimilitha & Sanjana

Congratulations to Nimilitha and Sanjana for completing their MTech degrees! Sanjana also received a Silver Medal for securing the top rank in the MTech (Medical Biotech) class.

July 12, 2014

Group Lunch at Athidhi

Group lunch at Athidhi. Welcome back to Sanjana and Yogeeshwar for PhD and Nimilitha for JRF. Congratulations to Preethi for her permanent position at Syngene. New additions: Abhishek and Bharathi.

June 26, 2014

Summer Research Symposium – TIFR Center, Hyderabad

Narendar, Nimilitha, and Sanjana's first poster presentation at the Summer Research Symposium conducted by the TIFR Center for Interdisciplinary Sciences, Hyderabad.

March 5, 2014

Excellence in Academics Award – Sanjana

Congratulations to Sanjana for receiving the Excellence in Academics Award, presented by Dr. R. Chidambaram, Principal Scientific Adviser to the Government of India, on the 6th Foundation Day of IIT Hyderabad.

December 17, 2013

Innovative Young Biotechnologist Award 2012 – Thenmalar

Thenmalar received the Innovative Young Biotechnologist Award 2012 from DBT, Government of India. The award was conferred by Shri Sudini Jaipal Reddy, Hon'ble Union Minister for Science & Technology and Earth Sciences.

December 15, 2013

Group Lunch at A Lounge

Group lunch at A Lounge. New additions: Venkat and Preethi.

October 26, 2013

Double Rainbow Captured at IITH

Nature's wonder captured at IITH between 4:45–5:00 PM - heavy rains gave way to a stunning double rainbow.

October 16, 2013

Setting Up Wet Lab at Kandi

Setting up our wet lab at Kandi. New addition: Yogeeshwar.

June 8, 2013

Group Lunch at De Banyan

Group lunch at De Banyan. New additions: Nimilitha and Sanjana.

December 29, 2012

Narendar Joins the Lab

Narendar joined our lab for his PhD, eager to begin his work on macromolecular structure and dynamics. All the best for the new endeavor!

May 7, 2012

Summer Intern – Noorain Khan

Noorain Khan, a B.Tech. graduate from P.A. College of Engineering Mangalore, joined our lab as a summer intern to work on the structure and dynamics of nucleic acids. Welcome, Noorain - have fun!

January 19–21, 2012

Best Oral Presentation Award – IBS Annual Meeting, Chennai

Thenmalar delivered an oral presentation at the Annual Meeting of the Indian Biophysical Society 2012 in Chennai and won the Best Oral Presentation Award!

December 12–17, 2011

Lab Activity Begins – International NMR Workshop, TIFR Hyderabad

Our lab's journey began with Thenmalar attending the International NMR Workshop organized by TIFR Hyderabad. Great interactions with NMR colleagues from India and abroad, especially with Profs. R. V. Hosur and Peter Guntert.

Opportunities

PhD positions open

Highly self-motivated, hard-working and enthusiastic individuals who have a strong interest in solving challenging biological problems using an interdisciplinary approach are encouraged to apply.

Contact Us

Primary Contacts

Follow Our Research

Professor's Office Hover for details
BT315, BTBM Building

Department of Biotechnology

IIT Hyderabad, Kandi 502284

(91) 40 2359 6154

tr@bt.iith.ac.in

Molecular Biophysics Lab Hover for details
BT223, BTBM Building

Department of Biotechnology

IIT Hyderabad, Kandi 502284

(91) 40 2359 8114

trlabservices@iith.ac.in

Send an Inquiry