2016
Protein Structure and Function: Looking through the Network of Side-Chain Interactions.
Bhattacharyya M, Ghosh S, Vishveshwara S. Protein Structure and Function: Looking through the Network of Side-Chain Interactions. Current Protein And Peptide Science 2016, 17: 4-25. PMID: 26412788, DOI: 10.2174/1389203716666150923105727.Peer-Reviewed Original ResearchConceptsNetwork theoryImportant problemComplex biological problemsProtein structure networksBipartite networksStructure networkEquilibrium structureModel validationDifferent schemesBiological problemsProblemNetwork approachTheoryNetwork metricsGeneral applicationComplex phenomenonGeneral featuresFormalismNetworkLarge numberProtein structureGeometrySpecific featuresBiological dataEnsemble
2012
Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach
Bhattacharyya M, Upadhyay R, Vishveshwara S. Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach. PLOS ONE 2012, 7: e51676. PMID: 23284738, PMCID: PMC3524241, DOI: 10.1371/journal.pone.0051676.Peer-Reviewed Original Research
2011
Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism
Bhattacharyya M, Vishveshwara S. Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism. Biochemistry 2011, 50: 6225-6236. PMID: 21650159, DOI: 10.1021/bi200306u.Peer-Reviewed Original ResearchConceptsPyrrolysyl-tRNA synthetaseDimeric proteinFunctioning of proteinsSequence/structureAllosteric regulationAllosteric communicationAnticodon recognitionTRNA synthetasesImportant residuesAllosteric mechanismKey residuesSubtle rearrangementsProteinKey playersPyrrolysineFunctional aspectsSynthetaseResiduesAtypical enzymeGlobal perturbationsComprehensive viewComplexesStructure networkMolecular dynamics simulationsPylRS