Computational Biology and Bioinformatics

Prof. Saraswathi Vishveshwara Laboratory

Molecular Biophysics Unit, IISc, Bangalore, India

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Publications by SV's Group

2015-2023

2007-2014

2006-2007

2005-2006

2002-2004

2000-2001

1996-1999

Posters and Conferences

Invited Talks

Publications (2015-2023)

Are microtubules electron-based topological insulators?
European Physical Letters (EPL), 143 (2023) 46001, doi: 10.1209/0295-5075/acec94
Subramanyan, V., Kay L. Kirkpatrick, K.L., Vishveshwara, S., and Vishveshwara, Sm.,(2023)
Comparison of structural networks across homologous proteins.
Proteins:SFB doi: 10.1002/prot.26650. Epub ahead of print. PMID: 38058245
Prabantu, V.M., Gadiyaram,V., Vishveshwara, S., Srinivasan, N.,(2023)
Understanding structural variability in proteins using protein structural networks.
CRSB 4: 134-145. https://doi.org/10.1016/j.crstbi.2022.04.002
Prabantu, V.M., Gadiyaram,V., Vishveshwara, S., Srinivasan, N., (2022)
Gefitinib Inhibits Rifampicin-Induced CYP3A4 Gene Expression in Human Hepatocytes.
ACS Omega 2022 7 (38), 34034-34044, DOI:10.1021/acsomega.2c03270
Kodye L. Abbott, Salamat, J.M., Flannery, P.C., Chaudhury, C.S., Chandran, A., Vishveshwara, S., Mani, S., Huang, J., Tiwari, A.K., and Pondugula, S.R., (2022)
Insights into Mechanisms and Models for Studying Neurological Adverse Events Mediated by Pharmacokinetic Interactions between Clinical Drugs and Illicit Substances of Herbal and Fungal Origin.
Medicinal Herbs and Fungi. Springer,Singapore. doi.org/10.1007/978-981-33-4141-8_5
Salamat, J.M., Chandran A. Vishveshwara S., et. al.,In: Agrawal D.C., Dhanasekaran M. (eds) (2021)
Network Re-Wiring During Allostery and Protein-Protein Interactions: A Graph Spectral Approach
Methods in Molecular Biology, vol 2253. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1154-8_7
Gadiyaram, V., Dighe, A., Ghosh, S., Vishveshwara, S. (2021) In: Di Paola L., Giuliani A. (eds)
Surveying the Side-Chain Network Approach to Protein Structure and Dynamics: The SARS-CoV-2 Spike Protein as an Illustrative Case.
Front. Mol. Biosci. 7:596945. doi: 10.3389/fmolb.2020.596945
Halder, A., Anto, A., Subramanyan, V., Bhattacharyya, M., Vishveshwara, S., and Vishveshwara, Sm., (2020)
Targeting the pregnane X receptor using microbial metabolite mimicry
EMBO Mol Med 12:e11621, doi.org/10.15252/emmm.201911621
Zdenek Dvorák, Aneesh Chandran, Saraswathi Vishveshwara, Sridhar Mani (Total of 22 groups contributed, our contribution is towards ligand docking studies), (2020)
From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses
J Chem. Inf. Model. 2019, 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)
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.
Gadiyaram, V., Dighe, A., Vishveshwara, S., (2018)
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.
Sci Rep 8, 9939 (2018). https://doi.org/10.1038/s41598-018-26812-8
Keasar, C., McGuffin, L.J., Wallner, B. et al. [A total of 16 groups contributed, Authors from our group(IISc): B. K. Dhanasekaran, Sambit Ghosh, Soma Ghosh & Saraswathi Vishveshwara]
Validation of Protein Structure Models using Network Similarity Score
Proteins: Structure, Function, and Bioinformatics. 85:1759–1776. doi: 10.1002/prot.25332.
Ghosh S., Gadiyaram V. and Vishveshwara S., (2017)
A graph spectral-based scoring scheme for network comparison.
Journal of Complex Networks, 5(2), pp.219-244. doi.org/10.1093/comnet/cnw016.
Gadiyaram V., Ghosh S., and Vishveshwara S. (2017)
Protein Structure and Function: Looking through the Network of Side-Chain Interactions
Curr Protein Pept Sci. 17(1):4-25.
Bhattacharyya M., Ghosh S., Vishveshwara S. (2016)
The flexibility and dynamics of protein disulfide isomerase
Proteins: Structure, Function, and Bioinformatics. 84:1776–1785. doi: 10.1002/prot.25159.
Romer R A., Wells S A, Jimenez-Roldan E., Bhattacharyya M., Vishveshwara S and Freedman R B. (2016)
Exploration of the conformational landscape in pregnane X receptor reveals a new binding pocket
Protein Sci. 25(11):1989-2005. doi: 10.1002/pro.3012.
Chandran A., Vishveshwara S. (2016)
Mechanism of Iron-Dependent Repressor (IdeR) Activation and DNA Binding: A Molecular Dynamics and Protein Structure Network Study
PLoS Comput Biol. 11(12):e1004500. doi:10.1371/journal.pcbi.1004500
Ghosh S., Chandra N., Vishweshwara S. (2015)

Publications (2007-2014)

Will be updated soon!

Publications (2006-2007)

Characterization of the backbone geometry of protein native state structures
Proteins: Structure, Function, and Bioinformatics 64 (4), 992-1000 (2006)
K. V. Brinda, and Saraswathi Vishveshwara
Dynamics of Lysozyme Structure Network: Probing the Process of Unfolding
Biophysical Journal, 92, 2523-2535 (2007)
Amit Ghosh, Brinda K.V. and Saraswathi Vishveshwara
Structure Networks in E.coli Glutaminyl tRNA Synthetase: Effects of ligand binding
Proteins: Structure, Function, and Bioinformatics Volume 68(2), 541 - 550 (2007)
Sathyapriya R and Saraswathi Vishveshwara
Insight into the Early Stages of Thermal Unfolding of Peanut Agglutinin by Molecular Dynamics Simulations
Proteins: Structure, Function, and Bioinformatics ,69 (1), 32-42 (2007)
Priti Hansia, Sagarika Dev, Avadhesha Surolia, and Saraswathi Vishveshwara
A Method for Computing the Inter-residue Interaction Potentials for Reduced Amino Acid Alphabet
J. Biosciences 32(5), 883-889 (2007)
Abhinav Luthra, Anupam Nath Jha, , G. K. Ananthasuresh and SaraswathiiVishveswara
Protein sequence design based on the topology of the native state structure
Journal of Theoretical Biology 248(1), 81-90 (2007)
Anupam Nath Jha, G. K. Ananthasuresh and Saraswathi Vishveshwara
Communication pathways from the anti-codon region to the aminoacylation site in Methionyl tRNA Synthetase: Molecular dynamics simulations and the structure network analysis
PNAS (in press)
Amit Ghosh and Saraswathi Vishveshwara
Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis
PloS ONE (in press)
Verkhedkar.K, Raman.K, Chandra N and Vishveshwara.S

Publications (2005-2006)

Correlation of the Side-Chain Hubs with the Functional Residues in DNA Binding Protein Structures
J. Chem. Inf. ModelVolume 46, Issue 1 (January 23, 2006).123-129
R. Sathyapriya, K. V. Brinda, and Saraswathi Vishveshwara (PDF)
Tryptophan-water interaction in Monellin: Hydration patterns from molecular dynamics simulation
Chem. Phys. Lett2006;420: 517-522.
Priti Hansia, Saraswathi Vishveshwara and Samir Kumar Pal (PDF)
Ab initio studies on the tri- and diphosphate fragments of adenosin e triphosphate
Biophys Chem.2006 Jan 20;119(2) :127-36
Priti Hansia, Guruprasad N and Saraswathi Vishveshwara (PDF)
A Deterministic Optimization Approach to Protein Sequence Design Using Continuous Models
The International Journal of Robotics Research2005, 24(2-3), 109-130
Sung K. Koh, G. K. Ananthasuresh & Vishveshwara S. (PDF)
Short hydrogen bonds in proteins.
FEBS J. 2005 Apr;272(8):1819-32
R.Sathyapriya, Vishveshwara S. (PDF)
A Network Representation of Protein Structures: Implications for Protein Stability
Biophysical Journal 2005, 89, P4159-4170
Brinda K. V. and Saraswathi Vishveshwara (PDF)
Oligomeric protein structure networks: Insights into protein-protein interactions.
BMC Bioinformatics 2005, 6:296
Brinda K.V. and Vishveshwara S (PDF)
Identification of Domains and Domain Interface Residues in Multidomain Proteins from Graph Spectral Method.
Proteins: Struct. Funct. Bioinfo.2005, 59(3), 616-626.
Sistla R. K., Brinda K.V. & Vishveshwara S. (PDF)
Insights into the quaternary association of proteins through structure graphs: A case study of lectins.
Biochemical Journal 2005, 391, 1-15(Journal Cover Illustration).
Brinda K.V., Surolia A. & Vishveshwara S. (PDF)
A Graph Spectral Analysis of the Structural Similarity Network of Protein Chains
Proteins: Struct. Funct. Bioinfo.2005, 61(1), 152-163
Krishnadev O., Brinda K.V. & Vishveshwara S. (PDF)
Dynamics of the native and the ligand-bound structures of eosinophil cationic protein: Network of hydrogen bonds at the catalytic site
Journal of Biomolecular Structure & Dynamics22,(6),657-671, 2005
Sanjeev B.S. & Vishveshwara S. (PDF)

Publications (2002-2004)

Interaction of DNA with clusters of amino acids in proteins
Nucleic Acids Research 2004 Aug 9;32(14):4109-18
R.Sathyapriya and Saraswathi Vishveshwara (PDF)
Determinants of quaternary association in legume lectins
Protein Sci. 2004 Jul;13(7):1735-49
Brinda KV, Mitra N, Surolia A, Vishveshwara S. (PDF)
Protein-Water Interactions in Ribonuclease A and Angiogenin: A Molecular Dynamics Study.
Proteins:SFB 2004 Jun 1;55(4):915-23
Sanjeev BS, Vishveshwara S. (PDF)
Stability and dynamics of domain-swapped Bovine-Seminal ribonuclease
Chemistry & Biodiversity 2004 May;1(5):802-818
Kalyan S Chakraborti, Sanjeev BS and Vishveshwara S. (PDF)
Protein Structure: Insights from Graph Theory
Jl Th Comp Chem. 2002 Jul;1(1):187-211
Vishveshwara S, Brinda KV, Kannan N. (PDF)
Essential dynamics and sidechain hydrogen bond cluster studies on eosinophil cationic protein
Eur. Phys. J. D 2002 Sep;20(3):601-608
Sanjeev BS and Vishveshwara S. (PDF)
Analysis of homodimeric protein interfaces by graph-spectral methods.
Protein Eng. 2002 Apr;15(4):265-77.
Brinda KV, Kannan N and Vishveshwara S. (PDF)
Conformational transitions in eosinophil cationic protein: A molecular dynamics study in aqueous environment
JBSD 2004 Oct;22(2);171-182
Sanjeev BS and Vishveshwara S.

Publications (2000-2001)

Computer modeling and molecular dynamics simulations of ligand bound complexes of bovine angiogenin: dinucleotide topology at the active site of RNase a family proteins.
Proteins: Structure, Function and Genetics2001 Oct 1;45(1):30-39
Madhusudhan MS, Sanjeev BS and Vishveshwara S. (PDF)
Deducing hydration sites of a protein from molecular dynamics simulations.
J Biomol Struct Dyn.2001 Aug;19(1):105-14.
Madhusudhan MS and Vishveshwara S. (PDF)
A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands.
Indian J Biochem Biophys.2001 Feb-Apr;38(1-2):27-33.
Madhusudhan MS, Vishveshwara S, Das A, Kalra P and Jayaram B.
Clusters in alpha/beta barrel proteins: implications for protein structure, function, and folding: a graph theoretical approach.
Proteins. 2001 May 1;43(2):103-12.
Kannan N, Selvaraj S, Gromiha MM and Vishveshwara S.
Short-strong hydrogen bonds and a low barrier transition state for the proton transfer reaction in RNase A catalysis: A quantum chemical study.
Biophys Chem.2001 Feb 15;89(2-3):105-17.
Vishveshwara S, Madhusudhan MS and Maizel JV Jr.
Stabilizing interactions in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: a graph spectral and point mutation study.
Protein Sci.2001 Jan;10(1):46-54.
Kannan N, Chander P, Ghosh P, Vishveshwara S and Chatterji D.
Sequence design in lattice models by graph theoretical methods
JCP2001, Jan 22; 114(4):1906-14.
Sanjeev BS, Patra SM and Vishveshwara S.
Computer modeling of human angiogenin-dinucleotide substrate interaction.
Proteins.2001 Jan 1;42(1):125-35.
Madhusudhan MS and Vishveshwara S.
Aromatic clusters: a determinant of thermal stability of thermophilic proteins.
Protein Eng.2000 Nov;13(11):753-61.
Kannan N and Vishveshwara S. (PDF)
Logos for amino-acid preferences in different backbone packing density regions of protein structural classes.
Acta Crystallogr D Biol Crystallogr.2000 Sep;56 ( Pt 9):1156-65.
Kannan N, Schneider TD and Vishveshwara S.
Backbone cluster identification in proteins by a graph theoretical method.
Biophys Chem.2000 Feb 14;84(1):13-25.
Patra SM and Vishveshwara S.

Publications (1996-1999)

Computer Modeling of Protein-Ligand Interaction" in Perspectives in Structural Biology
Indian Academy of Sciences and University Press 669-679, 1999.
Edited by M. Vijayan, N. Yathindra and A.S. Kolaskar
Identification of side-chain clusters in protein structures by a graph spectral method.
J Mol Biol.1999 Sep 17;292(2):441-64.
Kannan N and Vishveshwara S.
Classification of polymer structures by graph theory
International Journal of Quantum Chemistry71, 349-356 (1999).
S.M. Patra and Vishveshwara S
Comparison of the dynamics of bovine and human angiogenin: a molecular dynamics study.
Biopolymers.1999 Feb;49(2):131-44.
Madhusudhan MS, Vishveshwara S.
Modeling of angiogenin - 3-NMP complex.
J Biomol Struct Dyn.1998 Dec;16(3):715-22.
Madhusudhan MS, Vishveshwara S.
The role of Lysine-41 in Rnase A Catalysis- A quantum chemical study on the active site-l igand complex
Journal of Molecular Structure471, 1-11 (1998)
S. Vishveshwara, R. Jacob, G. Nadig and J. V. Maizel
Structure based design of model proteins
Proteins: Structure Function and Genetics31,10-20 (1998).
J.R. Banavar, M. Cieplak, A. Maritan, G. Nadig and S. Vishveshwara
Effects of substrate binding on the dynamics of RNase A: Molecular dynamics simulations o f UpA bound and native RNase A
Biopolymers42, 505-520 (1997)
Gautham Nadig and Saraswathi Vishveshwara
Protein Dynamics: Molecular simulations of RNase A and related proteins
Indian Ins titute of Science Journal77, 327-338 (1997).
G.Nadig, R.Varadarajan and Vishveshwara S
Design of rapidly folding protein-like heteropolymer chains and their cell dynamics: A l attice model study
Indian Institute of Science Journal77, 339-352 (1997).
Sarasw athi Vishveshwara, Indira Shrivastava, Marek Cieplak and Jayanth R Banavar
Determinants of Backbone packing in Globular Proteins: An Analysis of Spatial Neighbours
Acta CrystallographicaD53, 627-637 (1997).
S K Panjikar, Margaret Biswas and Saraswathi Vishveshwara
Cell Dynamics of Model Proteins.
Phys Rev Lett.1996 Oct 21;77(17):3681-3684.
Cieplak M, Vishveshwara S, Banavar JR.
Dynamics of Ribonuclease A and Ribonuclease S: Computational and experimental studies
Protein Science.5, 2104-2114 (1996).
G Nadig, GS Rathnaparki, R.Varadarajan and S Vishveshwara
Stability of Trans-membrane helices: A molecular dynamics study on the isolated helices of Bacteriorhodopsin
Biopolymers38, 401-421 (1996)
Lakshmanan K Iyer and Saraswathi Vishveshwara
Threonine mutations in proline helix II of bacteriorhodopsin: A molecular dynamics study
Journal of Molecular Structure (TheoChem)361, 269-281 (1996)
Lakshmanan.K.Iyer and Saraswathi Vishveshwara
Conformational Study of Valinomycin_A Molecular Dynamics Approach
Biophysical Chemistry57, 163-175 (1996)
S. Shobana and Saraswathi Vishveshwara

Posters and Conferences

Structure networks of Aminoacyl t-RNA synthetases: Insights into amino acid and t-RNA rec ognition presented in the '21st International t-RNA Workshop Proceedings, p171' from Dec 2nd -7th, 2005 at Indian Institute of Science, Bangalore, India by Sathyapriya R and Saraswathi V ishveshwara
Dynamics of t-RNA Synthetases presented in the '21st International t-RNA Workshop Proceed ings, p105' from Dec 2nd-7th, 2005 at Indian Institute of Science, Bangalore, India by Amit G hosh, Priti Hansia and Saraswathi Vishveshwara
Network topology of protein structures presented in 229th ACS National Meeting at San Die go, USA, John Pople Memorial Symposium from March 13-17, 2005 by S. Vishveshwara and K.V. Bri nda
Interaction of DNA with clusters of amino acids in proteins presented in the Internationa l Society of Molecular Biology (ISMB) meeting (ISMB-ECCB-04) held at Glasgow, Scotland from 3 1st July- 4th Aug 2004 by Brinda KV and Saraswathi Vishveshwara.
Analysis of protein interfaces using graph spectral methods presented at the 2nd conferen ce on Modeling of protein interactions in genomes from 27th-30th June 2003 at State Universit y of New York, Stony Brook, NY, USA by Brinda KV and Saraswathi Vishveshwara

Invited Talks

"Network topology of protein structures" in 229th ACS National Meeting at San Diego, USA, John Pople Memorial Symposium from March 13-17, 2005 by Saraswathi Vishveshwara
"Interaction of DNA with clusters of amino acids in proteins" in the 4th Indo-US Workshop in Mathematical Chemistry, at University of Pune from Jan 8-12,2005, India by Sathyapriya R
"Protein Structure Graphs and Networks" at Second Indo-French Bioinformatics Meeting Immunology & Molecular Biology Workshop, IFBM, Reunion, 10-12 December 2004 by Saraswathi Vishveshwara
"Inter-residue interactions in proteins" at Discussion Meeting on Intermolecular Interactions, Coorg, Karnataka, India, 30th November to 3rd December 2003 by Saraswathi Vishveshwara
"Graph Theory and the structure of biomolecules" at The 69th Annual Meeting of the Indian Academy of Sciences, Guwahati, India, November 21-23, 2003 by Saraswathi Vishveshwara
"Bioinformatics appraoch to protein structure, function and folding" at Workshop on Bioinformatics organized by Mauritius Research Council, Mauritius, September 4, 2003 by Saraswathi Vishveshwara
"Hydration patterns in Ribonuclease- A family proteins” at International workshop on Proteomics, ICTP, Trieste, Italy, May 15, 2003 by Saraswathi Vishveshwara
"Protein-protein interaction from graph spectral method" at International workshop on Proteomics, ICTP, Trieste, Italy, May 13, 2003 by Saraswathi Vishveshwara
"An insight into Protein structure, function and Stability- A Graph Theoretic Approach" at Symposium on Protein structure, Folding and Design, ICTP,Trieste, Italy, June 11-22, 2001 by Saraswathi Vishveshwara
"Cluster Identification in Protein Structures by Graph Theoretical Method" at National Seminar on Recent Trends in Crystallography , Biophysics and Computational Biology, NCBS_IISc. Bangalore, India, April 24-26, 2000 by Saraswathi Vishveshwara
"Graph Theory- A novel approach for cluster identification in Protein structures" at National workshop on Computer modelling- Bioinformatics, March 2001, IISc Bangalore, India by Saraswathi Vishveshwara