Saraswathi Vishveshwara - Publications

Affiliations: 
Molecular Biophysics Unit Indian Institute of Science, Bengaluru, Karnataka, India 

91 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Prabantu VM, Gadiyaram V, Vishveshwara S, Srinivasan N. Comparison of structural networks across homologous proteins. Proteins. PMID 38058245 DOI: 10.1002/prot.26650  0.371
2022 Prabantu VM, Gadiyaram V, Vishveshwara S, Srinivasan N. Understanding structural variability in proteins using protein structural networks. Current Research in Structural Biology. 4: 134-145. PMID 35586857 DOI: 10.1016/j.crstbi.2022.04.002  0.385
2021 Gadiyaram V, Dighe A, Ghosh S, Vishveshwara S. Network Re-Wiring During Allostery and Protein-Protein Interactions: A Graph Spectral Approach. Methods in Molecular Biology (Clifton, N.J.). 2253: 89-112. PMID 33315220 DOI: 10.1007/978-1-0716-1154-8_7  0.311
2020 Halder A, Anto A, Subramanyan V, Bhattacharyya M, Vishveshwara S, Vishveshwara S. Surveying the Side-Chain Network Approach to Protein Structure and Dynamics: The SARS-CoV-2 Spike Protein as an Illustrative Case. Frontiers in Molecular Biosciences. 7: 596945. PMID 33392257 DOI: 10.3389/fmolb.2020.596945  0.332
2019 Gadiyaram V, Vishveshwara S, Vishveshwara S. From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses. Journal of Chemical Information and Modeling. PMID 30912941 DOI: 10.1021/Acs.Jcim.9B00002  0.423
2019 Vishveshwara S, Dighe A, Gadiyaram V. Graph Spectral Properties of the Sidechain Networks of Protein Structures: Implications to Allostery and Structure Comparison Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.2504  0.406
2019 Gadiyaram V, Dighe A, Vishveshwara S. Identification of crucial elements for network integrity: a perturbation approach through graph spectral method International Journal of Advances in Engineering Sciences and Applied Mathematics. 11: 1-14. DOI: 10.1007/S12572-018-0236-7  0.343
2017 Ghosh S, Gadiyaram V, Vishveshwara S. Validation of Protein Structure Models using Network Similarity Score. Proteins. PMID 28598579 DOI: 10.1002/prot.25332  0.365
2016 Bhattacharyya M, Ghosh S, Vishveshwara S. Protein Structure and Function: Looking through the Network of Side-Chain Interactions. Current Protein & Peptide Science. 17: 4-25. PMID 26412788  0.326
2015 Ghosh S, Chandra N, Vishveshwara S. Investigating the Mechanism of Iron Dependent Repressor (IDER) Activation and DNA Binding Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.2068  0.352
2013 Bhattacharyya M, Bhat CR, Vishveshwara S. An automated approach to network features of protein structure ensembles. Protein Science : a Publication of the Protein Society. 22: 1399-416. PMID 23934896 DOI: 10.1002/pro.2333  0.331
2013 Chatterjee S, Ghosh S, Vishveshwara S. Network properties of decoys and CASP predicted models: A comparison with native protein structures Molecular Biosystems. 9: 1774-1788. PMID 23694935 DOI: 10.1039/c3mb70157c  0.341
2013 Ghosh S, Chatterjee S, Vishveshwara S. Network properties to distinguish native structures from non-native structures F1000research. 4. DOI: 10.7490/F1000Research.1093575.1  0.373
2013 Chatterjee S, Ghosh S, Vishveshwara S. 167 Network properties of decoy and CASP predicted models: a comparison with native protein structures Journal of Biomolecular Structure & Dynamics. 31: 108-109. DOI: 10.1080/07391102.2013.786409  0.438
2012 Bhattacharyya M, Upadhyay R, Vishveshwara S. Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach. Plos One. 7: e51676. PMID 23284738 DOI: 10.1371/journal.pone.0051676  0.327
2012 Vijayabaskar MS, Vishveshwara S. Insights into the fold organization of tim barrel from interaction energy based structure networks Plos Computational Biology. 8. PMID 22615547 DOI: 10.1371/journal.pcbi.1002505  0.346
2012 Chatterjee S, Bhattacharyya M, Vishveshwara S. Network properties of protein-decoy structures. Journal of Biomolecular Structure & Dynamics. 29: 606-22. PMID 22545992 DOI: 10.1080/07391102.2011.672625  0.366
2011 Ghosh A, Sakaguchi R, Liu C, Vishveshwara S, Hou YM. Allosteric communication in cysteinyl tRNA synthetase: a network of direct and indirect readout. The Journal of Biological Chemistry. 286: 37721-31. PMID 21890630 DOI: 10.1074/jbc.M111.246702  0.338
2011 Bhattacharyya M, Vishveshwara S. Probing the allosteric mechanism in pyrrolysyl-tRNA synthetase using energy-weighted network formalism Biochemistry. 50: 6225-6236. PMID 21650159 DOI: 10.1021/bi200306u  0.37
2011 Bhattacharyya M, Vishveshwara S. Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions Molecular Biosystems. 7: 2320-2330. PMID 21617814 DOI: 10.1039/c1mb05038a  0.338
2011 Sukhwal A, Bhattacharyya M, Vishveshwara S. Network approach for capturing ligand-induced subtle global changes in protein structures Acta Crystallographica Section D: Biological Crystallography. 67: 429-439. PMID 21543845 DOI: 10.1107/S0907444911007062  0.355
2011 Vijayabaskar MS, Niranjan V, Vishveshwara S. GraProStr - graphs of protein structures: A tool for constructing the graphs and generating graph parameters for protein structures Open Bioinformatics Journal. 5: 53-58. DOI: 10.2174/1875036201105010053  0.318
2010 Vijayabaskar MS, Vishveshwara S. Interaction energy based protein structure networks Biophysical Journal. 99: 3704-3715. PMID 21112295 DOI: 10.1016/J.Bpj.2010.08.079  0.483
2010 Bhattacharyya M, Vishveshwara S. Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis. Bmc Structural Biology. 10: 27. PMID 20704697 DOI: 10.1186/1472-6807-10-27  0.341
2010 Vijayabaskar MS, Vishveshwara S. Comparative analysis of thermophilic and mesophilic proteins using Protein energy networks Bmc Bioinformatics. 11. PMID 20122223 DOI: 10.1186/1471-2105-11-S1-S49  0.448
2010 Brinda KV, Vishveshwara S, Vishveshwara S. Random network behaviour of protein structures. Molecular Biosystems. 6: 391-8. PMID 20094659 DOI: 10.1039/B903019K  0.471
2010 Jha AN, Vishveshwara S, Banavar JR. Amino acid interaction preferences in proteins. Protein Science : a Publication of the Protein Society. 19: 603-16. PMID 20073083 DOI: 10.1002/Pro.339  0.383
2010 Bhattacharyya M, Ghosh A, Hansia P, Vishveshwara S. Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks. Proteins. 78: 506-17. PMID 19768679 DOI: 10.1002/Prot.22573  0.484
2010 Bhattacharyya M, Vishveshwara S. Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis Bmc Structural Biology. 10. DOI: 10.1186/1472-6807-10-27  0.331
2010 Pieniazek SN, Bhattacharyya M, Vishveshwara S, Hingorani M, Beveridge DL. Recognition and Signaling in DNA Mismatch Repair: Interdomain Communication in T. Aquaticus Muts Proteins Biophysical Journal. 98: 568a-569a. DOI: 10.1016/J.Bpj.2009.12.3084  0.357
2010 Vijayabaskar MS, Vishveshwara S. Construction of Energy Based Protein Structure Networks: Application in the Comparative Analysis of Thermophiles and Mesophiles Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.2089  0.464
2009 Hansia P, Ghosh A, Vishveshwara S. Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks. Molecular Biosystems. 5: 1860-72. PMID 19763332 DOI: 10.1039/B903807H  0.454
2009 Deb D, Vishveshwara S, Vishveshwara S. Understanding protein structure from a percolation perspective. Biophysical Journal. 97: 1787-94. PMID 19751685 DOI: 10.1016/J.Bpj.2009.07.016  0.461
2009 Jha AN, Ananthasuresh GK, Vishveshwara S. A search for energy minimized sequences of proteins. Plos One. 4: e6684. PMID 19690619 DOI: 10.1371/Journal.Pone.0006684  0.358
2009 Jha AN, Vishveshwara S. Inter-helical interactions in membrane proteins: Analysis based on the local backbone geometry and the side chain interactions Journal of Biomolecular Structure and Dynamics. 26: 719-729. PMID 19385700 DOI: 10.1080/07391102.2009.10507284  0.375
2009 Vishveshwara S, Ghosh A, Hansia P. Intra and inter-molecular communications through protein structure network. Current Protein & Peptide Science. 10: 146-60. PMID 19355982 DOI: 10.2174/138920309787847590  0.462
2009 Bhattacharyya M, Vishveshwara S. Functional correlation of bacterial LuxS with their quaternary associations: Interface analysis of the structure networks Bmc Structural Biology. 9. PMID 19243584 DOI: 10.1186/1472-6807-9-8  0.447
2009 Gupta G, Vishveshwara S, Surolia A. Stability of dimeric interface in banana lectin: Insight from molecular dynamics simulations. Iubmb Life. 61: 252-60. PMID 19189367 DOI: 10.1002/Iub.162  0.423
2009 Gupta G, Vishveshwara S, Surolia A. Stability of dimeric interface in banana lectin: Insight from molecular dynamics simulations Iubmb Life. 61: 252-260. DOI: 10.1002/iub.162  0.327
2008 Ghosh A, Vishveshwara S. Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes. Biochemistry. 47: 11398-407. PMID 18842003 DOI: 10.1021/Bi8007559  0.429
2008 Chowdhury RP, Vijayabaskar MS, Vishveshwara S, Chatterji D. Molecular mechanism of in vitro oligomerization of Dps from Mycobacterium smegmatis: Mutations of the residues identified by "interface cluster" analysis Biochemistry. 47: 11110-11117. PMID 18826253 DOI: 10.1021/Bi801158E  0.393
2008 Sathyapriya R, Vijayabaskar MS, Vishveshwara S. Insights into protein-DNA interactions through structure network analysis Plos Computational Biology. 4. PMID 18773096 DOI: 10.1371/Journal.Pcbi.1000170  0.393
2007 Ghosh A, Vishveshwara S. A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis. Proceedings of the National Academy of Sciences of the United States of America. 104: 15711-6. PMID 17898174 DOI: 10.1073/Pnas.0704459104  0.382
2007 Verkhedkar KD, Raman K, Chandra NR, Vishveshwara S. Metabolome based reaction graphs of M. tuberculosis and M. leprae: a comparative network analysis. Plos One. 2: e881. PMID 17849010 DOI: 10.1371/Journal.Pone.0000881  0.318
2007 Hansia P, Dev S, Surolia A, Vishveshwara S. Insight into the early stages of thermal unfolding of peanut agglutinin by molecular dynamics simulations Proteins: Structure, Function and Genetics. 69: 32-42. PMID 17596827 DOI: 10.1002/Prot.21512  0.413
2007 Jha AN, Ananthasuresh GK, Vishveshwara S. Protein sequence design based on the topology of the native state structure. Journal of Theoretical Biology. 248: 81-90. PMID 17543996 DOI: 10.1016/J.Jtbi.2007.04.018  0.383
2007 Sathyapriya R, Vishveshwara S. Structure networks of E. coli glutaminyl-tRNA synthetase: Effects of ligand binding Proteins: Structure, Function and Genetics. 68: 541-550. PMID 17444518 DOI: 10.1002/Prot.21401  0.42
2007 Ghosh A, Brinda KV, Vishveshwara S. Dynamics of lysozyme structure network: probing the process of unfolding. Biophysical Journal. 92: 2523-35. PMID 17208969 DOI: 10.1529/Biophysj.106.099903  0.442
2006 Brinda KV, Vishveshwara S. Characterization of the backbone geometry of protein native state structures Proteins: Structure, Function and Genetics. 64: 992-1000. PMID 16779840 DOI: 10.1002/Prot.20998  0.46
2006 Sathyapriya R, Brinda KV, Vishveshwara S. Correlation of the side-chain hubs with the functional residues in DNA binding protein structures Journal of Chemical Information and Modeling. 46: 123-129. PMID 16426048 DOI: 10.1021/Ci050122G  0.448
2006 Hansia P, Vishveshwara S, Pal SK. Tryptophan-water interaction in Monellin: Hydration patterns from molecular dynamics simulation Chemical Physics Letters. 420: 512-517. DOI: 10.1016/J.Cplett.2006.01.012  0.328
2005 Brinda KV, Vishveshwara S. Oligomeric protein structure networks: Insights into protein-protein interactions Bmc Bioinformatics. 6. PMID 16336694 DOI: 10.1186/1471-2105-6-296  0.447
2005 Brinda KV, Vishveshwara S. A network representation of protein structures: Implications for protein stability Biophysical Journal. 89: 4159-4170. PMID 16150969 DOI: 10.1529/Biophysj.105.064485  0.459
2005 Krishnadev O, Brinda KV, Vishveshwara S. A graph spectral analysis of the structural similarity network of protein chains Proteins: Structure, Function and Genetics. 61: 152-163. PMID 16080147 DOI: 10.1002/Prot.20532  0.405
2005 Sanjeev BS, 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 and Dynamics. 22: 657-671. PMID 15842171 DOI: 10.1080/07391102.2005.10507033  0.436
2005 Rajagopal S, Vishveshwara S. Short hydrogen bonds in proteins Febs Journal. 272: 1819-1832. PMID 15819878 DOI: 10.1111/J.1742-4658.2005.04604.X  0.386
2005 Sistla RK, K V B, Vishveshwara S. Identification of domains and domain interface residues in multidomain proteins from graph spectral method. Proteins. 59: 616-26. PMID 15789418 DOI: 10.1002/Prot.20444  0.353
2005 Koh SK, Ananthasuresh GK, Vishveshwara S. A deterministic optimization approach to protein sequence design using continuous models International Journal of Robotics Research. 24: 109-130. DOI: 10.1177/0278364905050354  0.327
2004 Chakrabarti KS, Sanjeev BS, Vishveshwara S. Stability and dynamics of domain-swapped bovine-seminal ribonuclease Chemistry and Biodiversity. 1: 802-818. PMID 17191881 DOI: 10.1002/cbdv.200490062  0.328
2004 Sanjeev BS, Vishveshwara S. Conformational transitions in eosinophil cationic protein: A molecular dynamics study in aqueous environment Journal of Biomolecular Structure and Dynamics. 22: 171-182. PMID 15317478 DOI: 10.1080/07391102.2004.10506993  0.344
2002 Sanjeev BS, Vishveshwara S. Essential dynamics and sidechain hydrogen bond cluster studies on eosinophil cationic protein European Physical Journal D. 20: 601-608. DOI: 10.1140/epjd/e2002-00151-x  0.309
2001 Madhusudhan MS, Vishveshwara S. Deducing hydration sites of a protein from molecular dynamics simulations Journal of Biomolecular Structure and Dynamics. 19: 105-114. PMID 11565842 DOI: 10.1080/07391102.2001.10506724  0.316
1999 Madhusudhan MS, Vishveshwara S. Comparison of the dynamics of bovine and human angiogenin: A molecular dynamics study Biopolymers. 49: 131-144. PMID 10070263 DOI: 10.1002/(SICI)1097-0282(199902)49:2<131::AID-BIP3>3.0.CO;2-W  0.313
1998 Madhusudhan MS, Vishveshwara S. Modeling of angiogenin - 3'-NMP complex Journal of Biomolecular Structure and Dynamics. 16: 715-722. PMID 10052627 DOI: 10.1080/07391102.1998.10508283  0.326
1998 Iyer LK, Vishveshwara S. The stability of transmembrane helices: a molecular dynamics study on the isolated helices of bacteriorhodopsin. Biopolymers. 38: 401-422. PMID 8906975 DOI: 10.1002/(Sici)1097-0282(199603)38:3<401::Aid-Bip12>3.0.Co;2-F  0.389
1998 Vishveshwara S, Jacob R, Nadig G, Maizel JV. The role of lysine-41 in RNase A catalysis: A quantum chemical study on the active site-ligand complex Journal of Molecular Structure. 471: 1-11. DOI: 10.1016/S0022-2860(98)00388-3  0.37
1996 Shobana S, Vishveshwara S. Conformational study of valinomycin: A molecular dynamics approach Biophysical Chemistry. 57: 163-175. DOI: 10.1016/0301-4622(95)00061-5  0.4
1995 Seshadri K, Rao VS, Vishveshwara S. Interaction of substrate uridyl 3',5'-adenosine with ribonuclease A: a molecular dynamics study. Biophysical Journal. 69: 2185-94. PMID 8599627 DOI: 10.1016/S0006-3495(95)80094-9  0.396
1995 Iyer LK, Vishveshwara S. A model for transmembrane helix with a cis-Proline in the middle Febs Letters. 374: 21-24. PMID 7589504 DOI: 10.1016/0014-5793(95)01042-D  0.338
1995 Shrivastava I, Vishveshwara S, Cieplak M, Maritan A, Banavar JR. Lattice model for rapidly folding protein-like heteropolymers Proceedings of the National Academy of Sciences of the United States of America. 92: 9206-9209. PMID 7568102 DOI: 10.1073/Pnas.92.20.9206  0.364
1994 Seshadri K, Rao VS, Vishveshwara S. Characterization of substrate UpA binding to RNase A--computer modelling and energetics approach. Journal of Biomolecular Structure & Dynamics. 12: 581-603. PMID 7727060 DOI: 10.1080/07391102.1994.10508761  0.382
1994 Shobana S, Nadig G, Vishveshwara S. Effect of the valine-threonine constraint on the dynamics of the proline helix - A molecular dynamics study Proceedings of the Indian Academy of Sciences - Chemical Sciences. 106: 579-589. DOI: 10.1007/BF02840772  0.305
1993 Sankararamakrishnan R, Vishveshwara S. Characterization of proline-containing α-helix (helix F model of bacteriorhodopsin) by molecular dynamics studies Proteins: Structure, Function and Genetics. 15: 26-41. PMID 8451238 DOI: 10.1002/Prot.340150105  0.392
1993 Vishveshwara SS, Vishveshwara S. Effect of constraints by threonine on proline containing αa-helix-A molecular dynamics approach Biophysical Chemistry. 46: 77-89. PMID 8443337 DOI: 10.1016/0301-4622(93)87009-L  0.46
1993 Seshadri K, Balaji PV, Rao VS, Vishveshwara S. Computer modelling studies of ribonuclease A-pyrimidine nucleotide complexes. Journal of Biomolecular Structure & Dynamics. 11: 395-415. PMID 8286064 DOI: 10.1080/07391102.1993.10508734  0.34
1992 Sankararamakrishna R, Vishveshwara S. The structures of bacteriorhodopsin with different retinal-schiff base orientations - computer modeling and energy minimization studies Journal of Biomolecular Structure and Dynamics. 9: 1073-1094. PMID 1637503 DOI: 10.1080/07391102.1992.10507980  0.42
1992 Sankararamakrishnan R, Vishveshwara S. Geometry of proline-containing alpha-helices in proteins International Journal of Peptide and Protein Research. 39: 356-363. PMID 1428525 DOI: 10.1111/J.1399-3011.1992.Tb01595.X  0.383
1992 Seshadri K, Rao VS, Vishveshwara S. Molecular dynamics studies on nucleoside 2',3'-cyclic phosphates. Journal of Biomolecular Structure & Dynamics. 9: 1253-68. PMID 1322144 DOI: 10.1080/07391102.1992.10507990  0.333
1991 Sankararamakrishnan R, Sreerama N, Vishveshwara S. Characterization of proline-containing right-handed α-helix by molecular dynamics studies Biophysical Chemistry. 40: 97-108. DOI: 10.1016/0301-4622(91)85034-N  0.447
1990 Sankararamakrishnan R, Vishveshwara S. Conformational studies on peptides with proline in the right-handed α-helical region Biopolymers. 30: 287-298. PMID 2279068 DOI: 10.1002/Bip.360300307  0.348
1989 Ramakrishnan RS, Vishveshwara S. A hydrogen bonded chain in bactereorhodopsin by computer modelling approach Journal of Biomolecular Structure and Dynamics. 7: 187-205. PMID 2818868 DOI: 10.1080/07391102.1989.10507760  0.395
1989 Sreerama N, Vishveshwara S. Ab initio studies on proton transfer involving Schiff base and related nitrogen compounds Journal of Molecular Structure. 212: 53-60. DOI: 10.1016/0022-2860(89)85067-7  0.303
1989 Sreerama N, Vishveshwara S. An ab-initio study of the proton affinity of conjugated schiff-base and related nitrogen compounds: an analysis of the triggering site of bacteriorhodopsin Journal of Molecular Structure. 194: 61-72. DOI: 10.1016/0022-2860(89)80070-5  0.341
1985 Sreerama N, Vishveshwara S. An ab initio study of (CH⋯X)+ hydrogen bonds including biological systems Journal of Molecular Structure: Theochem. 133: 139-146. DOI: 10.1016/0166-1280(85)85012-0  0.305
1985 Sreerama N, Vishveshwara S. Studies involving the electrostatic potential of valinomycin Journal of Biosciences. 8: 315-327. DOI: 10.1007/Bf02703985  0.37
1985 Kaliannan P, Vishveshwara S, Rao VSR. Anomeric effect in phosphate moieties of carbohydrates: An Ab initio study International Journal of Quantum Chemistry. 27: 181-194. DOI: 10.1002/Qua.560270209  0.318
1984 Kaliannan P, Vishveshwara S, Rao VSR. Ab initio SCF-MO study on difluoromethanediol and difluorodimethoxymethane Journal of Molecular Structure: Theochem. 108: 281-291. DOI: 10.1016/0166-1280(84)85012-5  0.339
1983 Kaliannan P, Vishveshwara S, Rao VSR. Ab initio SCF-MO study of the molecular structures of aminomethanol, aminesulfonic acid and N-methyl-sulfamate Journal of Molecular Structure: Theochem. 105: 359-374. DOI: 10.1016/0166-1280(83)80214-0  0.365
1983 Vishveshwara S, Rao VSR. An ab initio study of the β-lactam structure Journal of Molecular Structure. 92: 19-29. DOI: 10.1016/0022-2860(83)90347-2  0.344
1983 Kaliannan P, Vishveshwara S, Rao VSR. Theoretical investigation of the structures of H2SO4, (CH30)2SO2 and CH30S03 - Journal of Molecular Structure. 92: 7-17. DOI: 10.1016/0022-2860(83)90346-0  0.363
1978 Vishveshwara S. Bond length distortions associated with torsion potentials; ab-initio studies on methanediol Chemical Physics Letters. 59: 30-32. DOI: 10.1016/0009-2614(78)85607-3  0.319
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