Saraswathi Vishveshwara

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PROTEIN STRUCTURE: INSIGHTS FROM GRAPH THEORY

Saraswathi Vishveshwara, K. V. Brinda, Natarajan Kannan, 2002 .

Network Re-Wiring During Allostery and Protein-Protein Interactions: A Graph Spectral Approach.

Saraswathi Vishveshwara, Sambit Ghosh, Vasundhara Gadiyaram, 2020, Methods in molecular biology.

A graph spectral analysis of the structural similarity network of protein chains

Saraswathi Vishveshwara, O Krishnadev, K V Brinda, 2005, Proteins.

A Deterministic Optimization Approach to Protein Sequence Design Using Continuous Models

G. K. Ananthasuresh, Saraswathi Vishveshwara, Sung Key Koh, 2005, Int. J. Robotics Res..

Mechanism of Iron-Dependent Repressor (IdeR) Activation and DNA Binding: A Molecular Dynamics and Protein Structure Network Study

Soma Ghosh, Nagasuma R. Chandra, Saraswathi Vishveshwara, 2015, PLoS Comput. Biol..

A network model to explore protein-DNA interface properties

Saraswathi Vishveshwara, Vijayabaskar, Sathyapriya, 2006 .

Insights into Protein–DNA Interactions through Structure Network Analysis

Saraswathi Vishveshwara, R. Sathyapriya, M. S. Vijayabaskar, 2008, PLoS Comput. Biol..

Surveying the Side-Chain Network Approach to Protein Structure and Dynamics: The SARS-CoV-2 Spike Protein as an Illustrative Case

Saraswathi Vishveshwara, Anushka Halder, Arinnia Anto, 2020, Frontiers in Molecular Biosciences.

Overview of the Protein Side chain Network Approach: Application to the Spike Glycoprotein of SARS-Cov2

Saraswathi Vishveshwara, Anushka Halder, Arinnia Anto, 2020 .

Validation of protein structure models using network similarity score

Sambit Ghosh, Saraswathi Vishveshwara, Vasundhara Gadiyaram, 2017, Proteins.

Oligomeric protein structure networks: insights into protein-protein interactions

Saraswathi Vishveshwara, K. V. Brinda, S. Vishveshwara, 2005, BMC Bioinformatics.

From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses

Saraswathi Vishveshwara, Vasundhara Gadiyaram, Smitha Vishveshwara, 2019, J. Chem. Inf. Model..

Identification of crucial elements for network integrity: a perturbation approach through graph spectral method

Saraswathi Vishveshwara, Vasundhara Gadiyaram, Anasuya Dighe, 2018, International Journal of Advances in Engineering Sciences and Applied Mathematics.

A graph spectral-based scoring scheme for network comparison

Sambit Ghosh, Saraswathi Vishveshwara, Vasundhara Gadiyaram, 2016, J. Complex Networks.

Random network behaviour of protein structures.

Saraswathi Vishveshwara, K V Brinda, Smitha Vishveshwara, 2009, Molecular bioSystems.

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Saraswathi Vishveshwara, M. S. Vijayabaskar, S. Vishveshwara, 2010, BMC Bioinformatics.

Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

Saraswathi Vishveshwara, M. S. Vijayabaskar, S. Vishveshwara, 2012, PLoS Comput. Biol..

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Adam Liwo, Yi He, Jilong Li, 2018, Scientific Reports.

Correlation of the Side-Chain Hubs with the Functional Residues in DNA Binding Protein Structures

Saraswathi Vishveshwara, K. V. Brinda, R. Sathyapriya, 2006, J. Chem. Inf. Model..

Protein structure and folding – simplicity within complexity

Saraswathi Vishveshwara, S. Vishveshwara, Jayanth R.Banavar, 2013, Journal of biomolecular structure & dynamics.

Metabolome Based Reaction Graphs of M. tuberculosis and M. leprae: A Comparative Network Analysis

Nagasuma R. Chandra, Saraswathi Vishveshwara, Karthik Raman, 2007, PloS one.

Structure‐based design of model proteins

Flavio Seno, Amos Maritan, Saraswathi Vishveshwara, 1998, Proteins.

Dynamics of lysozyme structure network: probing the process of unfolding.

Saraswathi Vishveshwara, S. Vishveshwara, Amit Ghosh, 2007, Biophysical journal.

Rule-based modelling of iron homeostasis in tuberculosis.

Saraswathi Vishveshwara, Nagasuma Chandra, N. Chandra, 2011, Molecular bioSystems.

Ranking the quality of protein structure models using sidechain based network properties

Saraswathi Vishveshwara, S. Vishveshwara, Soma Ghosh, 2014, F1000Research.

Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions.

Saraswathi Vishveshwara, Moitrayee Bhattacharyya, S. Vishveshwara, 2011, Molecular bioSystems.

Network properties of protein-decoy structures

Saraswathi Vishveshwara, Moitrayee Bhattacharyya, Subhojyoti Chatterjee, 2012, Journal of biomolecular structure & dynamics.

Identification of domains and domain interface residues in multidomain proteins from graph spectral method

Saraswathi Vishveshwara, S. Vishveshwara, Ramesh K. Sistla, 2005, Proteins.

Understanding protein structure from a percolation perspective.

Saraswathi Vishveshwara, Smitha Vishveshwara, Dhruba Deb, 2009, Biophysical journal.

Short hydrogen bonds in proteins

Saraswathi Vishveshwara, S. Vishveshwara, S. Rajagopal, 2005, The FEBS journal.

Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks.

Saraswathi Vishveshwara, Amit Ghosh, Priti Hansia, 2009, Molecular bioSystems.

Sequence design in lattice models by graph theoretical methods

Saraswathi Vishveshwara, Swarna M. Patra, B. S. Sanjeev, 2001 .

GraProStr - Graphs of Protein Structures: A Tool for Constructing the Graphs and Generating Graph Parameters for Protein Structures

Saraswathi Vishveshwara, Vidya Niranjan, S. Vishveshwara, 2011 .

Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions

Saraswathi Vishveshwara, Anupam Nath Jha, S. Vishveshwara, 2009, Journal of biomolecular structure & dynamics.

Interaction of DNA with clusters of amino acids in proteins.

Saraswathi Vishveshwara, R Sathyapriya, S. Vishveshwara, 2004, Nucleic acids research.

Classification of polymer structures by graph theory

Saraswathi Vishveshwara, Swarna M. Patra, 1999 .

An automated approach to network features of protein structure ensembles

Saraswathi Vishveshwara, Moitrayee Bhattacharyya, S. Vishveshwara, 2013, Protein science : a publication of the Protein Society.

Characterization of the backbone geometry of protein native state structures

Saraswathi Vishveshwara, S. Vishveshwara, Brinda K.V., 2006, Proteins.

Structure networks of E. coli glutaminyl‐tRNA synthetase: Effects of ligand binding

Saraswathi Vishveshwara, R Sathyapriya, S. Vishveshwara, 2007, Proteins.

Protein Structure and Function: Looking through the Network of Side-Chain Interactions.

Saraswathi Vishveshwara, Moitrayee Bhattacharyya, S. Vishveshwara, 2015, Current protein & peptide science.

Amino acid interaction preferences in proteins

Saraswathi Vishveshwara, J. Banavar, S. Vishveshwara, 2010, Protein science : a publication of the Protein Society.

Interaction energy based protein structure networks.

Saraswathi Vishveshwara, M S Vijayabaskar, S. Vishveshwara, 2010, Biophysical journal.