An automated approach to network features of protein structure ensembles
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Saraswathi Vishveshwara | Moitrayee Bhattacharyya | S. Vishveshwara | Moitrayee Bhattacharyya | Chanda R Bhat | Chanda R. Bhat
[1] Mark E. J. Newman,et al. Structure and Dynamics of Networks , 2009 .
[2] S. Vishveshwara,et al. Probing the allosteric mechanism in pyrrolysyl-tRNA synthetase using energy-weighted network formalism. , 2011, Biochemistry.
[3] Saraswathi Vishveshwara,et al. Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks. , 2009, Molecular bioSystems.
[4] S. Vishveshwara,et al. Network approach for capturing ligand-induced subtle global changes in protein structures. , 2011, Acta crystallographica. Section D, Biological crystallography.
[5] A. Atilgan,et al. Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. , 2006, Biophysical journal.
[6] S. Vishveshwara,et al. A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis , 2007, Proceedings of the National Academy of Sciences.
[7] T. Vicsek,et al. Uncovering the overlapping community structure of complex networks in nature and society , 2005, Nature.
[8] Victoria A. Higman,et al. Uncovering network systems within protein structures. , 2003, Journal of molecular biology.
[9] Rahul Raman,et al. Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds , 2010, PloS one.
[10] I. Bahar,et al. Global dynamics of proteins: bridging between structure and function. , 2010, Annual review of biophysics.
[11] C. Dominguez,et al. Solution structure of the ubiquitin-conjugating enzyme UbcH5B. , 2004, Journal of molecular biology.
[12] Fidel Ramírez,et al. Computing topological parameters of biological networks , 2008, Bioinform..
[13] S. Vishveshwara,et al. Identification of side-chain clusters in protein structures by a graph spectral method. , 1999, Journal of molecular biology.
[14] M J Sippl,et al. Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.
[15] Nadezhda T. Doncheva,et al. Analyzing and visualizing residue networks of protein structures. , 2011, Trends in biochemical sciences.
[16] M. Babu,et al. Molecular signatures of G-protein-coupled receptors , 2013, Nature.
[17] M. Grossmann,et al. G Protein-coupled Receptors , 1998, The Journal of Biological Chemistry.
[18] S. Vishveshwara,et al. Allostery and conformational free energy changes in human tryptophanyl‐tRNA synthetase from essential dynamics and structure networks , 2010, Proteins.
[19] Saraswathi Vishveshwara,et al. GraProStr - Graphs of Protein Structures: A Tool for Constructing the Graphs and Generating Graph Parameters for Protein Structures , 2011 .
[20] M. Rapé,et al. The Ubiquitin Code , 2012, Annual review of biochemistry.
[21] Illés J. Farkas,et al. CFinder: locating cliques and overlapping modules in biological networks , 2006, Bioinform..
[22] Mark E. J. Newman,et al. The Structure and Function of Complex Networks , 2003, SIAM Rev..
[23] Saraswathi Vishveshwara,et al. Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks , 2012, PLoS Comput. Biol..
[24] P. Schimmel. Development of tRNA synthetases and connection to genetic code and disease , 2008, Protein science : a publication of the Protein Society.
[25] Hongtao Yu,et al. Mechanistic insight into the allosteric activation of a ubiquitin-conjugating enzyme by RING-type ubiquitin ligases. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[26] Saraswathi Vishveshwara,et al. Understanding protein structure from a percolation perspective. , 2009, Biophysical journal.
[27] J. Skolnick,et al. TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.
[28] S. Cusack,et al. Class I tyrosyl‐tRNA synthetase has a class II mode of cognate tRNA recognition , 2002, The EMBO journal.
[29] Matteo Tiberti,et al. xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures , 2012, J. Chem. Inf. Model..
[30] Z. Luthey-Schulten,et al. Dynamical networks in tRNA:protein complexes , 2009, Proceedings of the National Academy of Sciences.
[31] Ali Rana Atilgan,et al. Local motifs in proteins combine to generate global functional moves. , 2012, Briefings in functional genomics.
[32] Shigeyuki Yokoyama,et al. Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion , 2003, Nature Structural Biology.
[33] William R Taylor. Protein Structure Comparison Using Bipartite Graph Matching and Its Application to Protein Structure Classification * , 2002, Molecular & Cellular Proteomics.
[34] L. Luttrell,et al. Allosteric Modulators of G Protein-Coupled Receptors: Future Therapeutics for Complex Physiological Disorders , 2009, Journal of Pharmacology and Experimental Therapeutics.
[35] Sharon L. Milgram,et al. The Small World Problem , 1967 .
[36] S. Rasmussen,et al. Crystal Structure of the β2Adrenergic Receptor-Gs protein complex , 2011, Nature.
[37] Saraswathi Vishveshwara,et al. Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions. , 2011, Molecular bioSystems.
[38] Zaida Luthey-Schulten,et al. NetworkView: 3D display and analysis of protein·RNA interaction networks , 2012, Bioinform..
[39] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[40] Saraswathi Vishveshwara,et al. Network properties of protein-decoy structures , 2012, Journal of biomolecular structure & dynamics.
[41] Jeffrey J. Gray,et al. Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins , 2009, PLoS Comput. Biol..
[42] P. Brick,et al. Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. , 1989, Journal of molecular biology.
[43] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[44] Saraswathi Vishveshwara,et al. PROTEIN STRUCTURE: INSIGHTS FROM GRAPH THEORY , 2002 .
[45] S. Vishveshwara,et al. Determinants of quaternary association in legume lectins , 2004, Protein science : a publication of the Protein Society.
[46] Gennady Verkhivker,et al. Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases , 2011, PLoS Comput. Biol..
[47] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[48] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[49] R. Stevens,et al. High-Resolution Crystal Structure of an Engineered Human β2-Adrenergic G Protein–Coupled Receptor , 2007, Science.
[50] R. Nussinov,et al. Allo-network drugs: harnessing allostery in cellular networks. , 2011, Trends in pharmacological sciences.
[51] S. Vishveshwara,et al. Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes. , 2008, Biochemistry.
[52] R. Nussinov,et al. Allosteric effects in the marginally stable von Hippel–Lindau tumor suppressor protein and allostery-based rescue mutant design , 2008, Proceedings of the National Academy of Sciences.
[53] A. Folkesson. IT and society , 2013 .
[54] S. Vishveshwara,et al. Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach , 2012, PloS one.