IISc MBU

Computational Biology and Bioinformatics

Prof. Saraswathi Vishveshwara Laboratory

Molecular Biophysics Unit, IISc, Bangalore, India


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Publications from SV Lab

    2011-2020

    2020
    2019
    • From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses
      J. Chem. Inf. Model. 59(5): 1715-1727. doi: 10.1021/acs.jcim.9b00002

      Vasundhara Gadiyaram, Smitha Vishveshwara and Saraswathi Vishveshwara (2019)

    • Belinostat, at Its Clinically Relevant Concentrations, Inhibits Rifampicin Induced CYP3A4 and MDR1 Gene Expression
      Mol Pharmacol. 95(3):324-334. doi: 10.1124/mol.118.114587.

      Kodye L Abbott, Chloe S Chaudhury, Natasha Narayanan, Aneesh Chandran, Saraswathi Vishveshwara, Zdenek Dvorak, Sridhar Mani, Satyanarayana R Pondugula,(2019)
    2018
    • An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
      SCIENTIFIC REPORTS | 8:9939 | doi: 10.1038/s41598-018-26812-8

      Chen Keasar.,.....................Saraswathi Vishveshwara., Dong Xu., Foldit Players consortium & Silvia N. Crivelli (Total of 16 groups contributed) (2018)

    • Identification of Crucial Elements for Network Integrity: A Perturbation Approach through Graph Spectral Method
      Int J Adv Eng Sci Appl Math. doi.org/10.1007/s12572-018-0236-7

      Vasundhara Gadiyaram, Anasuya Dighe and Saraswathi Vishveshwara,(2018)
    2017
    • Validation of protein structure models using network similarity score.
      Proteins. 2017 Jun 9. doi: 10.1002/prot.25332.

      Ghosh S, Gadiyaram V, Vishveshwara S.

    • A graph spectral-based scoring scheme for network comparison
      Journal of Complex Networks, Volume 5, Issue 2, 1 June 2017, Pages 219–244,

      Vasundhara Gadiyaram, Sambit Ghosh, Saraswathi Vishveshwara
    2016
    • Exploration of the conformational landscape in pregnane X receptor reveals a new binding pocket.
      Protein Sci. 2016 Nov;25(11):1989-2005. doi: 10.1002/pro.3012. Epub 2016 Aug 23.

      Chandran A and Vishveshwara S
    • The flexibility and dynamics of protein disulfide isomerase" Proteins: Structure, Function, and Bioinformatics.
      Proteins: Structure, Function, and Bioinformatics. 84:1776-1785.doi: 10.1002/prot.25159(2016) .

      Romer R A., Wells S A, Jimenez-Roldan E., Bhattacharyya M., Vishweshwara S and Freedman R B
    • Protein Structure and Function: Looking through the Network of Side-Chain Interactions.
      Curr Protein Pept Sci. 17(1):4-25 (2016).

      Bhattacharyya M., Ghosh S., Vishveshwara S.
    2015
    • Mechanism of Iron-Dependent Repressor (IdeR) Activation and DNA Binding: A Molecular Dynamics and Protein Structure Network Study.
      PLoS Comput Biol. 2015 Dec 23;11(12):e1004500. doi: 10.1371/journal.pcbi.1004500

      Ghosh S, Chandra N, Vishweswara S

    • Protein Structure and Function: Looking through the Network of Side-Chain Interactions
      Current Protein and Peptide Science (CPPS), 2015

      Bhattacharyya M, Ghosh S, Vishveshwara S

    • Dissecting Ligand Binding Sites: A Layer at a time
      Biophysical Journal, Vol. 108,(2), Supplement 1, p216a, (2015)

      Dighe, A; Chandra, N, Ananthasuresh, G.K., Vishveswara, S.
      Abstract
    2014
    • Ranking the quality of protein structure models using sidechain based network properties
      F1000Research 2014, 3:17 (doi: 10.12688/f1000research.3-17.v1) (2014)

      Ghosh S and Vishveshwara S.
    • Weighting schemes in metabolic graphs for identifying biochemical routes
      Systems and Synthetic Biology 8 (1): 47-57, (doi: 10.1007/s11693-013-9128-0) (2014)

      Ghosh S, Baloni P, Vishveshwara S, Chandra N.


    • A Histidine Aspartate Ionic Lock Gates the Iron Passage in Miniferritins from Mycobacterium smegmatis
      J. Biol. Chem. 289:11042-11058. (doi: 10.1074/jbc.M113.524421) (2014)

      Williams SM, Chandran AV, Vijayabaskar MS, Roy S, Balaram H, Vishveshwara S, Vijayan M, Chatterji D
    2013
    • An automated approack to network features of protein structure ensembles
      Protein Sci. doi: 10.1002/pro.2333 (2013)
      Bhattacharyya M, Bhat CR, Vishveshwara S.
    • Network properties of decoys and CASP predicted models: a comparison with native protein structures
      Mol Biosyst. 9(7):1774-88. doi: 10.1039/c3mb70157c. (2013)
      Chatterjee S, Ghosh S, Vishveshwara S.
    • Protein structure and folding- simplicity within complexity
      J Biomol Struct Dyn. 31(9), 073-975 (2013)
      Banavar J.R. and Vishveshwara S.
    • Distinctive contributions of the ribosomal P-site elements m2G966, m5C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli
      Nucleic Acids Res. 41(9):4963-75. doi: 10.1093/nar/gkt175 (2013)
      Arora S, Bhamidimarri SP, Bhattacharyya M, Govindan A, Weber MH, Varshney U, Vishveshwara S
    • Network properties of decoy and CASP predicted models: A comparison with native protein structures
      Albany 2013, Book of Abstracts, (2013)
      Chatterjee. S; Ghosh. S; Vishveshwara. S
    2012
    • Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks
      PLoS Comput Biol. 8(5):e1002505. (2012)
      Vijayabaskar MS and Vishveshwara S
    • Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach
      PLoS One. 7(12):e51676. doi: 10.1371/journal.pone.0051676. (2012)
      Bhattacharyya M, Upadhyay R, Vishveshwara S
    • Network Properties of Protein Decoy Structures
      J Biomol Struct Dyn. 29(6):606-622 (2012)
      Chatterjee S, Bhattacharyya M, Vishveshwara S


    2011

    • Allosteric communication in cysteinyl tRNA synthetase: A network of direct and indirect readout
      J Biol Chem. 28;286(43):37721-31 (2011)
      Ghosh A, Sakaguchi R, Liu C, Hou YM, Vishveshwara S
    • Rule-based modelling of iron homeostasis in tuberculosis
      Mol Biosyst, 7:2750-68 (2011)
      Ghosh S, Prasad KV, Vishveshwara S, Chandra N
    • Amino acid interaction preferences in helical membrane proteins
      Protein Eng Des Sel, 24:579-88 (2011)
      Jha AN, Banavar JR, Vishveshwara S
    • Probing the allosteric mechanism in Pyrrolysyl-tRNA synthetase using energy-weighted network formalism
      Biochemistry, 50:6225-36 (2011)
      Bhattacharyya M, Vishveshwara S
    • Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions
      Mol Biosyst, 7:2320-30 (2011)
      Bhattacharyya M, Vishveshwara S
    • Network approach for capturing ligand-induced subtle global changes in protein structures
      Acta Crystallogr D Biol Crystallogr, 67:429-39 (2011)
      Sukhwal A, Bhattacharyya M, Vishveshwara S



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