PhD Publications

Chromatin Structure and Dynamics

  • Ramachandran, S., Vogel, L., Strahl, B. D., and Dokholyan, N.V. “Thermodynamic stability of histone H3 is a necessary but not sufficient driving force for its evolutionary conservation”, Public Library of Science Computational Biology, 7(1): e1001042 (2011)  pubmed    journal

Ryanodine Receptor Structure and Function

  • Shirvanyants, D., Ramachandran, S., Mei, Y., Xu, L., Meissner, G., Dokholyan, N. V. “Pore dynamics and conductance of RyR1 transmembrane domain”, Biophysical Journal, 106(11):2375-84 (2014)  pubmed    journal
  • Ramachandran, S.*, Chakraborty, A.*, Xu, L.*, Mei, Y., Samso, M., Dokholyan, N. V., and Meissner, G. “Structural determinants of skeletal muscle ryanodine receptor gating”, Journal of Biological Chemistry, 288(9):6154-65 (2013)  pubmed    journal
  • Ramachandran, S., Serohijos, A. W. R., Xu, L., Meissner, G., and Dokholyan, N. V. “A structural model of the pore-forming region of the skeletal muscle Ryanodine receptor (RyR1)”, Public Library of Science Computational Biology 5: e1000367 (2009)  pubmed    journal
  • Meissner, G., Pasek, D. A., Yamaguchi, N., Ramachandran, S., Dokholyan, N. V., and Tripathy, A. “Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels”, Proteins: Structure, Function, and Bioinformatics, 74: 207-211 (2009)  pubmed    journal

Platinum Anticancer Drugs and DNA Structure

  • Ramachandran, S., Temple, B., Alexandrova, A.N., Chaney, S. G., and Dokholyan, N. V., “Recognition of platinum-DNA adducts by HMGB1a”, Biochemistry 51(38):7608-17 (2012)  pubmed    journal
  • King, C. L., Ramachandran, S., Chaney, S. G., Collins, L., Swenberg, J. A., deKrafft, K. E., Lin, W., Cicurel, L., and Barbier, M. “Debio 0507 primarily forms diaminocyclohexane-Pt-d(GpG) and -d(ApG) DNA adducts in HCT116 cells”, Cancer Chemotherapy and Pharmacology, 69(3):665-677 (2012)  pubmed    journal
  • Bhattacharyya D.*, Ramachandran S.*, Sharma S., Pathmasiri W., King C. L., Baskerville-Abraham I., Boysen G., Swenberg J. A., Campbell S. L., Dokholyan N. V., and Chaney S. G. “Flanking bases influence the nature of DNA distortion by oxaliplatin 1,2-intrastrand (GG) cross-links” Public Library of Science One, 6:e23582 (2011)  pubmed    journal
  • Ramachandran, S., Temple, B., Chaney, S. G., and Dokholyan, N. V. “Structural basis for the sequence dependent effects of Platinum-DNA adducts”, Nucleic Acids Research 37: 2434-2448 (2009)  pubmed    journal

Biomolecular Structural Modeling

  • Thompson PM, Ramachandran S, Case LB, Tolbert CE, Tandon A, Pershad M, Dokholyan NV, Waterman CM, Campbell SL. A Structural Model for Vinculin Insertion into PIP2-Containing Membranes and the Effect of Insertion on Vinculin Activation and Localization. Structure 2016 Dec 31 pubmed pdf
  • Wang, L., Xie, L., Ramachandran, S., Lee, Y., Yan, Z., Zhou, L., Krajewski, K., Liu, F., Zhu, C., Chen, D.J., Strahl, B.D., Jin, J., Dokholyan, N.V., Chen, X. “Non-canonical Bromodomain within DNA-PKcs Promotes DNA Damage Response and Radioresistance through Recognizing an IR-Induced Acetyl-Lysine on H2AX”, Chemical Biology 22(7):849-61 (2015)  pubmed    journal
  • Ramachandran, S.*, Ding, F.*, Weeks, K. M., and Dokholyan, N. V. “Statistical analysis of SHAPE-directed RNA secondary structure modeling”, Biochemistry, 52(4):596-9 (2013)  pubmed    journal
  • Shirvanyants, D., Ding, F., Tsao, D., Ramachandran, S., and Dokholyan, N. V. “DMD: an efficient and versatile simulation method for fine protein characterization”, Journal of Physical Chemistry B, 116(29):8375-8382 (2012)  pubmed    journal
  • Gyimesi G., Ramachandran S., Kota P., Dokholyan N. V., Sarkadi, B., and Hegedus T. “Molecular dynamics simulations of ABC transporters: the “bottom- open” structure may not correspond to a stable conformation” Biochimica et Biophysica Acta – Biomembranes, 1808:2954-2964 (2011)  pubmed    journal
  • Kota, P.*, Ding, F.*, Ramachandran, S.*, and  Dokholyan, N.V. “Gaia: automated quality assessment of protein structure models”, Bioinformatics, 27:2209-2215 (2011)  pubmed    journal
  • Ramachandran, S.*, Kota, P.*, Ding, F., and Dokholyan, N. V. “Automated minimization of steric clashes in protein structures”, Proteins: Structure, Function and Bioinformatics, 79(1): 261-70 (2011)  pubmed    journal
  • Jayanth, N., Ramachandran, S., and Puranik, M. “Solution structure of the DNA damage lesion, 8-oxoguanosine from ultraviolet resonance Raman spectroscopy”, Journal of Physical Chemistry 113 (8), 1459–1471 (2009)  pubmed    journal

*Equal Contribution


  • Redler R. L., Shirvanyants D., Dagliyan O., Din g F., Kim D. N., Kota P., Proctor E. A., Ramachandran S., Tandon A., Dokholyan N. V. “Computational approaches to understanding protein aggregation in neurodegeneration”, Journal of molecular cell biology 6(2):104-15 (2014)  pubmed    journal
  • Ramachandran S., and Dokholyan N. V. “Homology modeling: generating structural models to understand protein function and mechanism” in “Computational Modeling of Biological Systems: From Molecules to Pathways”, Editor: Dokholyan N. V., Springer Press (2012)  pdf
  • Chaney, S. G., Ramachandran, S., Sharma, S., Dokholyan, N. V., Temple, B., Bhattacharyya, D., Wu, Y., and Campbell, S. “Differences in Conformation and Conformational Dynamics Between Cisplatin and Oxaliplatin DNA Adducts” in “Platinum and Other Heavy Metal Compounds in Cancer Chemotherapy”, Editors: Bonetti, A., Leone, R., Muggia, F. M., and Howell, S. B., Humana Press, (2009) pdf


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