Browse by Author

Prabantu, Vasam Manjveekar and Gadiyaram, Vasundhara and Vishveshwara, Saraswathi and Srinivasan, Narayanaswamy (2022) Understanding structural variability in proteins using protein structural networks. In: Current Research in Structural Biology, 4 . pp. 134-145. ISSN 2665928X

Dvořák, Zdeněk and Kopp, Felix and Costello, Cait M and Kemp, Jazmin S and Li, Hao and Vrzalová, Aneta and Štěpánková, Martina and Bartoňková, Iveta and Jiskrová, Eva and Poulíková, Karolína and Vyhlídalová, Barbora and Nordstroem, Lars U and Karunaratne, Chamini V and Ranhotra, Harmit S and Mun, Kyu Shik and Naren, Anjaparavanda P and Murray, Iain A and Perdew, Gary H and Brtko, Julius and Toporova, Lucia and Schön, Arne and Wallace, Bret D and Walton, William G and Redinbo, Matthew R and Sun, Katherine and Beck, Amanda and Kortagere, Sandhya and Neary, Michelle C and Chandran, Aneesh and Vishveshwara, Saraswathi and Cavalluzzi, Maria M and Lentini, Giovanni and Cui, Julia Yue and Gu, Haiwei and March, John C and Chatterjee, Shirshendu and Matson, Adam and Wright, Dennis and Flannigan, Kyle L and Hirota, Simon A and Sartor, Ryan Balfour and Mani, Sridhar (2020) Targeting the pregnane X receptor using microbial metabolite mimicry. In: EMBO Molecular Medicine . ISSN 1757-4676

Gadiyaram, Vasundhara and Vishveshwara, Smitha and Vishveshwara, Saraswathi (2019) From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses. In: JOURNAL OF CHEMICAL INFORMATION AND MODELING, 59 (5, SI). pp. 1715-1727.

Vishveshwara, Saraswathi and Dighe, Anasuya and Gadiyaram, Vasundhara (2019) Graph Spectral Properties of the Sidechain Networks of Protein Structures: Implications to Allostery and Structure Comparison. In: 63rd Annual Meeting of the Biophysical-Society, 2 - 6 March, 2019, Baltimore, MD, 463A-464A.

Gadiyaram, Vasundhara and Ghosh, Sambit and Vishveshwara, Saraswathi (2017) A graph spectral-based scoring scheme for network comparison. In: Journal of Complex Networks, 5 (2). pp. 219-244. ISSN 2051-1310

Ghosh, Sambit and Gadiyaram, Vasundhara and Vishveshwara, Saraswathi (2017) Validation of protein structure models using network similarity score. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 85 (9). pp. 1759-1776.

Chandran, Aneesh and Vishveshwara, Saraswathi (2016) Exploration of the conformational landscape in pregnane X receptor reveals a new binding pocket. In: PROTEIN SCIENCE, 25 (11). pp. 1989-2005.

Dighe, Anasuya and Chandra, Nagasuma and Vishveshwara, Saraswathi and Ananthasuresh, GK (2015) Dissecting Ligand Binding Sites : A Layer at a Time. In: BIOPHYSICAL JOURNAL, 108 (2, 1). 216A.

Ghosh, Soma and Chandra, Nagasuma and Vishveshwara, Saraswathi (2015) Influence of iron on iron dependent repressor (IdeR) activation and DNA binding. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33 (1). p. 8.

Ghosh, Soma and Chandra, Nagasuma and Vishveshwara, Saraswathi (2015) Investigating the Mechanism of Iron Dependent Repressor (IDER) Activation and DNA Binding. In: BIOPHYSICAL JOURNAL, 108 (2, 1). 377A.

Bhattacharyya, Moitrayee and Ghosh, Soma and Vishveshwara, Saraswathi (2015) Protein Structure and Function: Looking through the Network of Side-Chain Interactions. In: CURRENT PROTEIN & PEPTIDE SCIENCE, 17 (1). pp. 4-25.

Williams, Sunanda Margrett and Chandran, Anu V and Vijayabaskar, Mahalingam S and Roy, Sourav and Balaram, Hemalatha and Vishveshwara, Saraswathi and Vijayan, Mamannamana and Chatterji, Dipankar (2014) A Histidine Aspartate Ionic Lock Gates the Iron Passage in Miniferritins from Mycobacterium smegmatis. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 289 (16). pp. 11042-11058.

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.

Ghosh, Soma and Vishveshwara, Saraswathi and Chandra, Nagasuma (2013) Inferring biochemical routes from biochemical networks. In: 4th Annual ORNL Biomedical Sciences and Engineering Conference on Collaborative Biomedical Innovations, MAY 21-23, 2013, Biomed Sci & Engn Ctr, Oak Ridge Natl Lab, Oak Ridge, TN.

Bhat, Chanda R and Bhattacharyya, Moitrayee and Vishveshwara, Saraswathi (2013) NON-GLYCINE RESIDUES IN THE DISALLOWED REGIONS OF THE RAMACHANDRAN MAP AND THEIR NEIGHBORHOOD PREFERENCES. In: Conference on Biomolecular Forms and Functions - A Celebration of 50 Years of the Ramachandran Map, JAN, 2013, Indian Inst Sci, Bangalore, INDIA, pp. 95-106.

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.

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.

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

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 .