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Number of items: 75.

Conference Paper

Ghosh, Amit and Vishveshwara, Saraswathi (2006) Modelling and molecular dynamics simulationof tRNA bound methionine tRNA synthetase. In: InCoB 2006 International Conference on Bioinformatics-2006, Dec 2006, New Delhi.

Jha, Anupam Nath and Vishveshwara, Saraswathi (2006) Protein sequence design based on the topology of the native-state structure. In: InCoB 2006 (International Conference on Bioinformatics-2006) New Delhi, Dec 2006, New Delhi.

Vishveshwara, Saraswathi (2006) Structure Networks of amino acyl-tRNA Synthetases: Insights into amino acid and tRNA recognition. In: Third Indo-French Bioinformatics Meeting (IFBM 2006) Bangalore, June 12-14 2006, Bangalore.

Vijayabaskar, MS and Vishveshwara, Saraswathi and Sathyapriya, * (2006) A network model to explore protein-DNA interface properties. In: InCoB 2006 (International Conference on Bioinformatics-2006) New Delhi, Dec 2006, New Delhi.

Journal Article

Arora, Smriti and Bhamidimarri, Satya Prathyusha and Bhattacharyya, Moitrayee and Govindan, Ashwin and Weber, Michael HW and Vishveshwara, Saraswathi and Varshney, Umesh (2013) Distinctive contributions of the ribosomal P-site elements m(2)G966, m(5)C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli. In: Nucleic Acids Research, 41 (9). pp. 4963-4975.

Banavar, Jayanth R and Vishveshwara, Saraswathi (2013) Protein structure and folding - simplicity within complexity. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31 (9, SI). pp. 973-975.

Bhattacharyya, Moitrayee and Bhat, Chanda R and Vishveshwara, Saraswathi (2013) An automated approach to network features of protein structure ensembles. In: PROTEIN SCIENCE, 22 (10). pp. 1399-1416.

Vijayabaskar, MS and Vishveshwara, Saraswathi (2012) Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks. In: PLOS COMPUTATIONAL BIOLOGY, 8 (5).

Chatterjee, Subhojyoti and Bhattacharyya, Moitrayee and Vishveshwara, Saraswathi (2012) Network properties of protein-decoy structures. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29 (6). pp. 606-622.

Bhattacharyya, Moitrayee and Upadhyay, Roopali and Vishveshwara, Saraswathi (2012) Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach. In: PLOS ONE, 7 (12).

Ghosh, Amit and Sakaguchi, Reiko and Liu, Cuiping and Vishveshwara, Saraswathi and Hou, Ya-Ming (2011) Allosteric Communication in Cysteinyl tRNA Synthetase A NETWORK OF DIRECT AND INDIRECT READOUT. In: Journal of Biological Chemistry, 286 (43). pp. 37721-37731.

Jha, Anupam Nath and Vishveshwara, Saraswathi and Banavar, Jayanth R (2011) Amino acid interaction preferences in helical membrane proteins. In: Protein Engineering Design and Selection, 24 (8). pp. 579-588.

Sukhwal, Anshul and Bhattacharyya, Moitrayee and Vishveshwara, Saraswathi (2011) Network approach for capturing ligand-induced subtle global changes in protein structures. In: Acta Crystallographica Section D, 67 (Part 5). pp. 429-439.

Bhattacharyya, Moitrayee and Vishveshwara, Saraswathi (2011) Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions. In: Molecular BioSystems, 7 (7). pp. 2320-2330.

Ghosh, Soma and Prasad, KVS and Vishveshwara, Saraswathi and Chandra, Nagasuma (2011) Rule-based modelling of iron homeostasis in tuberculosis. In: Molecular BioSystems, 7 (10). pp. 2750-2768.

Vijayabaskar, MS and Vishveshwara, Saraswathi (2010) Interaction Energy Based Protein Structure Networks. In: Biophysical Journal, 99 (11). pp. 3704-3715.

Bhattacharyya, Moitrayee and Vishveshwara, Saraswathi (2010) Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis. In: BMC Structural Biology, 10 .

Jha, Anupam Nath and Vishveshwara, Saraswathi and Banavar, Jayanth R (2010) Amino acid interaction preferences in proteins. In: Protein Science, 19 (3). pp. 603-616.

Bhattacharyya, Moitrayee and Ghosh, Amit and Hansia, Priti and Vishveshwara, Saraswathi (2010) Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks. In: Proteins: Structure, Function, and Bioinformatics, 78 (3). pp. 506-517.

Vijayabaskar, MS and Vishveshwara, Saraswathi (2010) Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks. In: BMC Bioinformatics, 11 (Suppl.).

Vijayabaskar, MS and Vishveshwara, Saraswathi (2010) Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks. In: BMC Bioinformatics, 11 (Suppl.).

Brinda, KV and Vishveshwara, Saraswathi and Vishveshwara, Smitha (2010) Random network behaviour of protein structures. In: Molecular Biosystems, 6 (2). pp. 391-398.

Deb, Dhruba and Vishveshwara, Saraswathi and Vishveshwara, Smitha (2009) Understanding Protein Structure from a Percolation Perspective. In: Biophysical Journal, 97 (6). pp. 1787-1794.

Jha, Anupam Nath and Ananthasuresh, GK and Vishveshwara, Saraswathi (2009) A Search for Energy Minimized Sequences of Proteins. In: PLoS ONE, 4 (8).

Ghosh, Amit and Hansia, Priti and Vishveshwara, Saraswathi (2009) Allostery in tRNA Synthetases Elucidated from MD Simulations and Protein Structure Networks. In: Journal of biomolecular structure dynamics, 26 (6). p. 100.

Jha, Anupam Nath and Vishveshwara, Saraswathi (2009) Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions. In: Journal of Biomolecular Structure & Dynamics, 26 (6). pp. 719-729.

Vishveshwara, Saraswathi and Ghosh, Amit and Hansia, Priti (2009) Intra and Inter-Molecular Communications Through Protein Structure Network. In: Current Protein & Peptide Science, 10 (2). pp. 146-160.

Gupta, Garima and Vishveshwara, Saraswathi and Surolia, Avadhesha (2009) Stability of Dimeric Interface in Banana Lectin: Insight from Molecular Dynamics Simulations. In: IUBMB Life, 61 (3). pp. 252-260.

Bhattacharyya, Moitrayee and Vishveshwara, Saraswathi (2009) Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks. In: BMC Structural Biology, 9 . pp. 1-16.

Hansia, Priti and Ghosh, Amit and Vishveshwara, Saraswathi (2009) Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks. In: Molecular biosystems, 5 (12). pp. 1860-1872.

Ghosh, Amit and Vishveshwara, Saraswathi (2008) Variations in Clique and Community Patterns in Protein Structures during Allosteric Communication: Investigation of Dynamically Equilibrated Structures of Methionyl tRNA Synthetase Complexes. In: BIOCHEMISTRY, 47 (44). pp. 11398-11407.

Chowdhury, Rakhi Pait and Vijayabaskar,, MS and Vishveshwara, Saraswathi and Chatterji, Dipankar (2008) Molecular Mechanism of in Vitro oligomerization of Dps from Mycobacterium smegmatis:mutations of the residues identified by Interface Cluster analysis. In: Biochemistry, 47 (42). pp. 11110-11117.

Sathyapriya, R and Vijayabaskar, MS and Vishveshwara, Saraswathi (2008) Insights into Protein-DNA Interactions through Structure Network Analysis. In: PLoS Computational Biology, 4 (9). pp. 1-15.

Ghosh , Amit and Vishveshwara , Saraswathi (2007) Communication pathways from the anti-codon region to the aminoacylation site in Methionyl tRNA Synthetase: Molecular dynamics simulations and the structure network analysis. In: Proceedings of the National Academy of Sciences, 104 (40). pp. 15711-15716.

Hansia,, Priti and Dev, Sagarika and Surolia, Avadhesha and Vishveshwara, Saraswathi (2007) Insight into the early stages of thermal unfolding of peanut agglutinin by molecular dynamics simulations. In: Proteins: Structure, Function, and Genetics, 69 (1). pp. 32-42.

Ghosh, Amit and Vishveshwara, Saraswathi (2007) A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis. In: Proceedings of the National Academy of Sciences of the United States of America (PNAS), 104 (40). pp. 15711-15716.

Verkhedkar, K and Raman, K and Chandra, Nagasuma R and Vishveshwara, Saraswathi (2007) Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis. In: PLOS ONE, 2 (9).

Jha, Anupam Nath and Ananthasuresh, GK and Vishveshwara, Saraswathi (2007) Protein sequence design based on the topology of the native state structure. In: Journal of Theoretical Biology, 248 (1). pp. 81-90.

Ghosh, Amit and Brinda, KV and Vishveshwara, Saraswathi (2007) Dynamics of Lysozyme Structure Network: Probing the Process of Unfolding. In: Biophysical Journal, 92 . pp. 2523-2535.

Sathyapriya, R and Vishveshwara, Saraswathi (2007) Structure Networks of E. coli Glutaminyl-tRNA Synthetase: Effects of Ligand Binding. In: PROTEINS: Structure, Function, and Bioinformatics, 68 . pp. 541-550.

Brinda, KV and Vishveshwara, Saraswathi (2006) Characterization of the backbone geometry of protein native state structures. In: Proteins: Structure, Function, and Bioinformatics, 64 (4). pp. 992-1000.

Hansia, Priti and Vishveshwara, Saraswathi and Pal, Samir Kumar (2006) Tryptophan-water interaction in Monellin:Hydration patterns from molecular dynamics simulations. In: Chemical Physics Letters, 420 (4-6). pp. 512-517.

Hansia, Priti and Vishveshwara, Saraswathi and Pal, Samir Kumar (2006) Tryptophan–water interaction in Monellin: Hydration patterns from molecular dynamics simulation. In: Chemical Physics Letters, 420 (4-6). pp. 512-517.

Hansia, P and Guruprasad, N and Vishveshwara, Saraswathi (2006) Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate. In: Biophysical Chemistry, 119 (2). pp. 127-136.

Hansia, Priti and Guruprasad, N and Vishveshwara, Saraswathi (2006) Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate. In: Biophysical Chemistry, 119 (2). pp. 127-136.

Sathyapriya, R and Brinda, KV and Vishveshwara, Saraswathi (2006) Correlation of the Side-Chain Hubs with the Functional Residues in DNA Binding Protein Structures. In: Journal of Chemical Information and Modeling, 46 (1). pp. 123-129.

Brinda, KV and Vishveshwara, Saraswathi (2005) Oligomeric protein structure networks: insights into protein-protein interactions. In: BMC Bioinformatics, 6 .

Sistla, Ramesh K and Brinda, KV and Vishveshwara, Saraswathi (2005) Identification of Domains and Domain Interface Residues in Multidomain Proteins from Graph Spectral Method. In: Proteins-structure Function and Bioinformatics, 59 (3). pp. 616-626.

Rajagopal, Sathyapriya and Vishveshwara, Saraswathi (2005) Short hydrogen bonds in proteins. In: FEBS Journal, 272 (8). pp. 1819-1832.

Krishnadev, O and Brinda, KV and Vishveshwara, Saraswathi (2005) A Graph Spectral Analysis of the Structural Similarity Network of Protein Chains. In: Proteins: Structure, Function, and Bioinformatics, 61 . pp. 152-163.

Sathyapriya, R and Vishveshwara, Saraswathi (2004) Interaction of DNA with clusters of amino acids in proteins. In: Nucleic Acids Research, 32 (14). pp. 4109-4118.

Brinda, KV and Mitra, Nivedita and Surolia, Avadhesha and Vishveshwara, Saraswathi (2004) Determinants of quaternary association in legume lectins. In: Protein Science, 13 (7). pp. 1735-1749.

Chakrabarti, Kalyan S and Sanjeev, BS and Vishveshwara, Saraswathi (2004) Stability and Dynamics of Domain-Swapped Bovine-Seminal Ribonuclease. In: Chemistry and Biodiversity, 1 (5). pp. 802-818.

Kannan, Natarajan and Chander, Preethi and Ghosh, Pallavi and Vishveshwara, Saraswathi and Chatterji, Dipankar (2001) Stabilizing interactions in the dimer interface of \alpha-subunit in Escherichia coli RNA polymerase: A graph spectral and point mutation study. In: Protein Science, 10 (1). pp. 46-54.

Madhusudhan, MS and Vishveshwara, Saraswathi (1999) Comparison of the Dynamics of Bovine and Human Angiogenin: A Molecular Dynamics Study. In: Biopolymers, 49 (2). pp. 131-144.

Vishveshwara, Saraswathi and Jacob, Rebecca and Nadig, Gautham and Maizel Jr, Jacob V (1998) The role of lysine-41 in RNase A catalysis - A quantum chemical study on the active site ligand complex. In: Journal of Molecular Structure, 471 (1-3). 01-11.

Panjikar, Santosh K and Biswas, Margaret and Vishveshwara, Saraswathi (1997) Determinants of backbone packing in globular proteins: An analysis of spatial neighbours. In: Acta Crystallographica Section D-Biological Crystallography, 53 (Part 6). pp. 627-637.

Nadig, Nadig and Vishveshwara, Saraswathi (1997) Effects of substrate binding on the dynamics of RNase A: Molecular dynamics simulations of UpA bound and native RNase A. In: Biopolymers, 42 (5). pp. 505-520.

Cieplak, Marek and Vishveshwara, Saraswathi and Banavar, Jayanth R (1996) Cell Dynamics of Model Proteins. In: Physical Review Letters, 77 (17). pp. 3681-3684.

Nadig, Gautham and Ratnaparkhi, Girish S and Varadarajan, Raghavan and Vishveshwara, Saraswathi (1996) Dynamics of ribonuclease A and ribonuclease S: Computational and experimental studies. In: Protein Science, 05 (10). pp. 2104-2114.

Iyer, Lakshmanan K and Vishveshwara, Saraswathi (1996) The stability of transmembrane helices: A molecular dynamics study on the isolated helices of bacteriorhodopsin. In: Biopolymers, 38 (3). pp. 401-422.

Shobana, S and Vishveshwara, Saraswathi (1996) Conformational study of valinomycin: a molecular dynamics approach. In: Biophysical Chemistry, 57 (2-3). pp. 163-175.

Iyer, Lakshmanan K and Vishveshwara, Saraswathi (1995) A model for transmembrane helix with a cis-Proline in the middle. In: Febs Letters, 374 (1). pp. 21-24.

Ma, Wen-Jong and Iyer, Lakshmanan K and Vishveshwara, Saraswathi and Koplik, Joel and Banavar, Jayanth R (1995) Molecular-dynamics studies of systems of confined dumbbell molecules. In: Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 51 (1). pp. 441-453.

Vishveshwara, Shobana S and Vishveshwara, Saraswathi (1993) Effect of constraints by threonine on proline containing αa-helix—A molecular dynamics approach. In: Biophysical Chemistry, 46 (1). pp. 77-89.

Sankararamakrishnan, R and Vishveshwara, Saraswathi (1993) Characterization of Proline-Containing a-Helix (Helix F Model of Bacteriorhodopsin) by Molecular Dynamics Studies. In: Proteins: Structure, Function, and Genetics, 15 (1). pp. 26-41.

Sankararamakrishnan, R and Vishveshwara, Saraswathi (1990) Conformational Studies on Peptides with Proline in the Right-Handed \alpha -Helical Region. In: Biopolymers, 30 (3-4). pp. 287-298.

Sreerama, N and Vishveshwara, Saraswathi (1989) An ab-initio study of the proton affinity of conjugated schiff-base and related nitrogen compounds: an analysis of the triggering site of bacteriorhodopsin. In: Journal of Molecular Structure, 194 . pp. 61-72.

Sankara-Ramakrishnan, R and Vishveshwara, Saraswathi (1989) A hydrogen bonded chain in bactereorhodopsin by computer modeling approach. In: Journal of Biomolecular Structure & Dynamics, 7 (1). pp. 187-205.

Sreerama, N and Vishveshwara, Saraswathi (1987) Molecular mechanism of facilitated transport by carrier ionophores: A study of energetics. In: Journal of Biosciences, 12 (3). pp. 175-189.

Dinesha, KV and Iyer, Suman B and Vishveshwara, Saraswathi (1986) Energy expressions for atomic configurations in the L-S coupling scheme. In: International Journal of Quantum Chemistry, 30 (6). pp. 783-790.

Vishveshwara, Saraswathi and Rao, VSR (1982) Anomeric effect in sulfur-containing systems: An Ab-initio study. In: Carbohydrate Research, 104 (1). pp. 21-32.

Vishveshwara, Saraswathi (1978) Ab-initio molecular orbital studies on C---H…X hydrogen bonded systemsstar. In: Chemical Physics Letters, 59 (1). pp. 26-29.

Vishveshwara, Saraswathi (1978) Bond length distortions associated with torsion potentials; ab-initio studies on methanedio. In: Chemical Physics Letters, 59 (1). 30-32 .

Editorials/Short Communications

Vishveshwara, Saraswathi and Rao, VSR (1981) Ab-initio studies of anomeric effect in thiosugars. In: Current Science (Bangalore), 50 (22). pp. 991-992.

This list was generated on Thu Apr 17 22:15:07 2014 IST.