Computational Biology and Bioinformatics
Prof. Saraswathi Vishveshwara Laboratory
Molecular Biophysics Unit, IISc, Bangalore, India
Publications from SV Lab
- Comparative Analysis of Thermophilic and Mesophilic Proteins using Protein Energy Networks
BMC Bioinformatics, 11(Suppl 1):S49 (2010)
Vijayabaskar M.S., Saraswathi Vishveshwara
- Random Network Behaviour of Protein Structures
Mol. Biosyst. 6, 391-398 (2010)
Brinda K.V., Saraswathi Vishveshwara, Smitha Vishveshwara
- Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis
BMC Structural Biology 10:27 (2010)
Bhattacharyya M and Vishveshwara S
- Amino acid interaction preferences in proteins
Protein Science, 19:603—616 (2010)
Anupam Nath Jha, Vishveshwara S and Banavar J.R.
- Interaction Energy based Protein Structure Networks
Biophysical Journal, 99: 3704-3715 (2010)
Vijayabaskar M.S. And Vishveshwara S
- Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks
Proteins, 78:506-17 (2010)
Bhattacharyya M, Ghosh A, Hansia P, Vishveshwara S
- Stability of dimeric interface in banana lectin: Insight from molecular dynamics simulations
IUBMB life 61(3):252-60.(2009)
Gupta Garima, Vishveshwara Saraswathi, Surolia Avadhesha
- Inter-helical interactions in membrane proteins: analysis based on the local backbone geometry and the side chain interactions
J Biomol Struct Dyn. 26(6):719-29 (2009)
Anupam Nath Jha and Saraswathi Vishveshwara
- A search for energy minimized sequences of proteins.
PLoS One. 2009 Aug 19;4(8):e6684. doi: 10.1371/journal.pone.0006684.
Jha AN, Ananthasuresh GK, Vishveshwara S.
- Functional correlation of bacterial LuxS with their quaternary associations: Interface analysis of the structure network
BMC Structural Biology 9:8 .(2009)
Moitrayee Bhattacharyya and Saraswathi Vishveshwara
- Intra and Inter-molecular communications through Protein Structure Networks
Invited Review in Current Protein and Peptide Science (CPPS) , 10 (2): 146-60.(2009)
Saraswathi Vishveshwara, Amit Ghosh and Priti Hansia
- Insights into Protein-DNA Interactions through Structure Network Analysis
PloS Computational Biology 4(9): e1000170(2008)
R Sathyapriya, MS Vijayabaskar and Saraswathi Vishveshwara
- Molecular Mechanism of in-Vitro Oligomerization of Dps from Mycobacterium smegmatis: Mutations of the Residues Identified by "Interface Cluster" Analysis
Biochemistry , 47, 11110-17.(2008)
Rakhi Pait Chowdhury,M. S. Vijayabaskar, Saraswathi Vishveshwara, and Dipankar Chatterji
- Variations in clique and community patterns in protein structures during allosteric communication: Investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes
Biochemistry , 47 (44):11398-407 (2008)
Amit Ghosh and Saraswathi Vishveshwara
- Dynamics of Lysozyme Structure Network: Probing the Process of Unfolding
Biophysical Journal, 92, 2523-35 (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 - 50 (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 Saraswathi Vishveshwara
- 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 published September 26, 2007, 10.1073/pnas.0704459104 ( Biophysics )
Amit Ghosh and Saraswathi Vishveshwara
- Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis
PloS ONE 12;2(9):e881
Verkhedkar.K, Raman.K, Chandra N and Vishveshwara.S
- 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
- 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
- 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
- Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate
Biophys Chem.2006 Jan 20;119(2):127-36
Priti Hansia, Guruprasad N and Saraswathi Vishveshwara
- 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.
Short hydrogen bonds in proteins.
FEBS J.2005 Apr;272(8):1819-32
R.Sathyapriya, Vishveshwara S.
- A Network Representation of Protein Structures: Implications for Protein Stability
Biophysical Journal 2005, 89, P4159-4170
Brinda K. V. and Saraswathi Vishveshwara
Oligomeric protein structure networks: Insights into protein-protein interactions.
BMC Bioinformatics 2005, 6:296
Brinda K.V. and Vishveshwara S
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.
- 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.
- 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.
- 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.
Copyright © 2015 SV Laboratory, All Rights Reserved. Maintained By SV Group