Publications

From IITH

(* Equal contribution)

  • Murali Aadhitya, MS, Patro, LPP*, Uttamrao, PP* and Rathinavelan, T. (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". Environmental Microbiology Reports (Accepted)
  • Murali Aadhitya, MS, Patro, LPP*, Uttamrao, PP* and Rathinavelan, T. (2022), "Geographical distribution of SARS-CoV-2 amino acids mutations and the concomitant evolution of seven distinct clades in non-human hosts". Zoonoses and Public Health, https://doi.org/10.1111/zph.12971
  • Patro, LPP and Rathinavelan, T. (2022), "STRIDER: Steric hindrance and metal coordination identifier". Comput Biol Chem, doi.org/10.1016/j.compbiolchem.2022.107686
  • Ajjugal, Y. and Rathinavelan, T. (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". Comput Struct Biotechnol J., doi.org/10.1016/j.csbj.2021.07.018
  • P. P. Uttamrao, C. Sathyaseelan*, L. P. P. Patro*, T. Rathinavelan (2021), "Revelation of potent epitopes present in unannotated ORF antigens of SARS-CoV-2 using immunoinformatics approach for the polyvalent epitope vaccine design". Frontiers in Immunology, doi.org/10.3389/fimmu.2021.692937
  • Patro, L.P.P.*, Sathyaseelan, C.*, Uttamrao, P.P.* and Rathinavelan, T. (2021), "Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades" . Infection, Genetics and Evolution., doi.org/10.1016/j.meegid.2021.104973.
  • Patro, L.P.P.*, Sathyaseelan, C.*, Uttamrao, P.P.* and Rathinavelan, T. (2021), "The evolving proteome of SARS-CoV-2 predominantly uses mutation combination strategy for survival" . Comput Struct Biotechnol J., doi: 10.1016/j.csbj.2021.05.054.
  • Sathyaseelan, C.*, Vijayakumar, V.* and Rathinavelan, T. (2021), "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" . J Mol Biol., 433(11):166629. doi.org/10.1016/j.jmb.2020.08.014
  • Ajjugal, Y.*, Kolimi, N.* and Rathinavelan, T. (2021), "Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS" . Sci Rep., 11(1):8163. doi.org/10.1038/s41598-021-87097-y
  • Ajjugal, Y.*, and Rathinavelan, T. (2021), "Sequence dependent influence of an A… A mismatch in a DNA duplex: An insight into the recognition by hZαADAR1 protein" . J Struct Biol., 213(1):107678. doi.org/10.1016/j.jsb.2020.107678
  • Ajjugal, Y.*, Tomar, K.* Rao, D.K., and Rathinavelan, T. (2021), "Spontaneous and frequent conformational dynamics induced by A… A mismatch in d (CAA)· d (TAG) duplex" . Sci Rep., 11(1):3689. doi.org/10.1038/s41598-021-82669-4
  • Patro, L.P.P.*, Sudhakar, K.U.* and Rathinavelan, T. (2020), "K-PAM: A unified platform to distinguish Klebsiella species K-and O-antigen types, model antigen structures and identify hypervirulent strains" . Sci Rep., 7;10(1):16732. doi.org/10.1038/s41598-020-73360-1
  • Patro, L.P.P., and Rathinavelan, T. (2020), "STRIDER: Steric hindrance estimator" . BioRxiv., 2020.02. 07.931550. doi.org/10.1101/2020.02.07.931550
  • Patro, L.P.P., and Rathinavelan, T. (2019), "Targeting the sugary armor of klebsiella species" . Front Cell Infect Microbiol., 8,9-367. doi.org/10.3389/fcimb.2019.00367
  • Patro, L.P.P.*, Kumar, A.*, Kolimi, N.* and Rathinavelan, T. (2017), "3D-NuS: A Web Server for Automated Modeling and Visualization of non-canonical 3-Dimensional Nucleic Acid Structures" . J Mol Biol., 429,2438-2448. doi.org/10.1016/j.jmb.2017.06.013
  • Kolimi, N.*, Ajjugal. Y* and Rathinavelan, T. (2017), "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". J Biol Chem. 292, 18732-18746 doi.org/10.1074/jbc.M117.796235
  • Sachdeva, S.*, Palur, R.V.*, Sudhakar, K.U.* and Rathinavelan, T. (2017), "E. coli group I capsular polysaccharide exportation nanomachinary as an antivirulent target in the perspective of emerging antimicrobial resistance". Front Microbiol 8:70. doi: doi.org/10.3389/fmicb.2017.00070. eCollection 2017.
  • Goldsmith, G., Rathinavelan, T. and Yathindra N. (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", PLoS One 11(3), e0152102 doi.org/10.1371/journal.pone.0152102
  • Sachdeva, S.*, Kolimi, N.*, Nair, S.A.* and Rathinavelan, T. (2016), "Key Diffusion Mechanisms Involved in Water Conduction of Wzi", Sci. Rep. 28157. doi.org/10.1038/srep28157
  • Kunduru, B.R.*, Nair, S.N.* and Rathinavelan, T. (2016), "EK3D: an E. coli K antigen 3-Dimensional Structure Database", Nucleic Acids Res. 44 (D1), D675-D681 doi.org/10.1093/nar/gkv1313
  • Khan, N.*, Kolimi, N* and Rathinavelan, T.* (2015), "Twisting Right To Left: A…A Mismatch In A CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation", PLoS Comput. Biol. Published: April 13, doi.org/10.1371/journal.pcbi.1004162
  • 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), "NMR Model of PrgI-SipD Interaction and its Implications in the Needle-Tip Assembly of the Salmonella Type III Secretion System", J. Mol. Biol. 426, 2958-69 (Continuation of KU Work) doi.org/10.1016/j.jmb.2014.06.009

From UM, IBAB & KU

  • Rathinavelan, T., Tang, C. and De Guzman, R.N. (2011), "Characterization of the Interaction between the Salmonella Type III Secretion System Tip Protein SipD and the Needle Protein PrgI by Paramagnetic Relaxation Enhancement", J. Biol. Chem. 286, 4922-30. doi.org/10.1074/jbc.M110.159434
  • Lim, K.H., Nagchowdhuri P., Rathinavelan, T. and W. Im (2010) "NMR Characterization of Hydrophobic Collapses in Amyloidogenic Partially Folded States and Their Implications for Protein Misfolding and Amyloid Formation", Biochem. Biophys. Res. Commun. 396, 800-05. doi.org/10.1016/j.bbrc.2010.04.137
  • Rathinavelan, T., Zhang, L., Picking, W.L., Weis, D.D., De Guzman, R.N. and Im, W. (2010), "A Repulsive Electrostatic Mechanism for Protein Export through the Type III Secretion Apparatus", Biophy. J. 98, 452-61 (Cover page article) (Highlighted paper). doi.org/10.1016/j.bpj.2009.10.030
  • Rathinavelan, T. and Im, W. (2008), "A Novel Strategy to Determine Protein Structures using Exclusively Residual Dipolar Coupling", J. Comput. Chem. 29, 1640-49. doi.org/10.1002/jcc.20923
  • Wang, Y., Ouellette, A.N., Egan, C.W., Rathinavelan, T., Im, W. and De Guzman, R.N. (2007), "Differences in the Electrostatic Surfaces of the Type III Secretion Needle Proteins", J. Mol. Biol., 371, 1304-14. doi.org/10.1016/j.jmb.2007.06.034
  • Rathinavelan, T. and Im, W. (2007), "Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination", J. Comput. Chem., 28, 1858-64. doi.org/10.1002/jcc.20712
  • Rathinavelan, T. and Yathindra, N. (2006), "Base triplet nonisomorphism strongly influences DNA triplex conformation: effect of nonisomorphic G* GC and A* AT triplets and bending of DNA triplexes", Biopolymers, 82, 443-61. doi.org/10.1002/bip.20484
  • Rathinavelan, T. and Yathindra, N. (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", FEBS J., 272, 4055-70. doi.org/10.1111/j.1742-4658.2005.04817.x
  • Thenmalarchelvi, R. and Yathindra, N. (2005), "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", Nucleic Acids Res., 35, 43-55. doi.org/10.1093/nar/gki143
  • Xodo, L.E, Rathinavelan, T., Quadrifoglio, F., Manzini, G., and Yathindra, N. (2001), "Targeting neighbouring poly(purine.pyrimidine) sequences located in the human bcr promoter by triplex-forming oligonucleotides", Eur. J. Biochem., 268, 656-64. doi.org/10.1046/j.1432-1327.2001.01919.x

Book Chapters

  • Rathinavelan, T. and Im, W. (2010), "A computational approach to explore protein translocation through type III secretion apparatus", In Quantum Bio-Informatics: From Quantum Information to Bio-Informatics, Eds. L. Accardi, W. Freudenberg, and M. Ohya 26, 453-63
  • Thenmalarchelvi, R. and Yathindra, N. (2003), ‘"Residual" Hoogsteen twist as a measure of nonisomorphism in DNA base triplets: Implications to sequence dependent DNA triplexes’, Recent Trends in Biophysical Research, Eds. Maiti, M., Suresh Kumar, G. and Das, S., 17-24, Publishers: Double A Work Station, Kolkata, India