Deciphering General Characteristics of Residues Constituting Allosteric Communication Paths
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Maksim Kouza | Anirban Banerji | Girik Malik | Irina A. Buhimschi | Andrzej Kloczkowski | A. Kloczkowski | M. Kouza | A. Banerji | I. Buhimschi | Girik Malik | Anirban Banerji
[1] D. Leitner,et al. Mass fractal dimension and the compactness of proteins. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.
[2] A. Atilgan,et al. Manipulation of conformational change in proteins by single-residue perturbations. , 2010, Biophysical journal.
[3] Lila M Gierasch,et al. The changing landscape of protein allostery. , 2006, Current opinion in structural biology.
[4] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[5] R. Nussinov,et al. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. , 2016, Chemical reviews.
[6] M. Friedman. A Comparison of Alternative Tests of Significance for the Problem of $m$ Rankings , 1940 .
[7] J. Changeux,et al. ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL. , 1965, Journal of molecular biology.
[8] Eugene I. Shakhnovich. Protein Folding Thermodynamics and Dynamics: Where Physics, Chemistry, and Biology Meet , 2006 .
[9] D. Koshland,et al. Comparison of experimental binding data and theoretical models in proteins containing subunits. , 1966, Biochemistry.
[10] L. Freeman,et al. Centrality in valued graphs: A measure of betweenness based on network flow , 1991 .
[11] R. Ranganathan,et al. Evolutionarily conserved pathways of energetic connectivity in protein families. , 1999, Science.
[12] Ruth Nussinov,et al. A Unified View of “How Allostery Works” , 2014, PLoS Comput. Biol..
[13] Lila M. Gierasch,et al. Sending Signals Dynamically , 2009, Science.
[14] R. Nussinov,et al. Allostery and population shift in drug discovery. , 2010, Current opinion in pharmacology.
[15] L. Freeman. Centrality in social networks conceptual clarification , 1978 .
[16] Janusz M Bujnicki,et al. Generalized protein structure prediction based on combination of fold‐recognition with de novo folding and evaluation of models , 2005, Proteins.
[17] K. Gurney,et al. Network ‘Small-World-Ness’: A Quantitative Method for Determining Canonical Network Equivalence , 2008, PloS one.
[18] A. Kolinski,et al. Characterization of protein-folding pathways by reduced-space modeling , 2007, Proceedings of the National Academy of Sciences.
[19] F. Wilcoxon. Individual Comparisons by Ranking Methods , 1945 .
[20] Adam Liwo,et al. Coarse-grained force field: general folding theory. , 2011, Physical chemistry chemical physics : PCCP.
[21] Ruth Nussinov,et al. Introduction to Protein Ensembles and Allostery. , 2016, Chemical reviews.
[22] Mateusz Kurcinski,et al. Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking. , 2015, Methods.
[23] R. Nussinov,et al. The origin of allosteric functional modulation: multiple pre-existing pathways. , 2009, Structure.
[24] Guang Song,et al. An enhanced elastic network model to represent the motions of domain‐swapped proteins , 2006, Proteins.
[25] S. Solla,et al. Self-sustained activity in a small-world network of excitable neurons. , 2003, Physical review letters.
[26] Ina Koch,et al. Enumerating all connected maximal common subgraphs in two graphs , 2001, Theor. Comput. Sci..
[27] Nikolay V Dokholyan,et al. Controlling Allosteric Networks in Proteins. , 2013, Chemical reviews.
[28] Andrzej Kolinski,et al. CABS-flex predictions of protein flexibility compared with NMR ensembles , 2014, Bioinform..
[29] I. Ghosh,et al. Revisiting the Myths of Protein Interior: Studying Proteins with Mass-Fractal Hydrophobicity-Fractal and Polarizability-Fractal Dimensions , 2009, PloS one.
[30] V. Traag,et al. Community detection in networks with positive and negative links. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.
[31] Peter Willett,et al. Maximum common subgraph isomorphism algorithms for the matching of chemical structures , 2002, J. Comput. Aided Mol. Des..
[32] Dominik Gront,et al. Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates , 2007, J. Comput. Chem..
[33] A Kolinski,et al. Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model. , 2017, Physical chemistry chemical physics : PCCP.
[34] M. Cieplak,et al. Proteins at air-water and oil-water interfaces in an all-atom model. , 2017, Physical chemistry chemical physics : PCCP.
[35] Indira Ghosh,et al. Fractal symmetry of protein interior: what have we learned? , 2011, Cellular and Molecular Life Sciences.
[36] P. Bonacich. Power and Centrality: A Family of Measures , 1987, American Journal of Sociology.
[37] Shlomi Reuveni,et al. Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure , 2010, Proceedings of the National Academy of Sciences.
[38] Andrzej Kloczkowski,et al. Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron , 2008, Proteins.
[39] D. Kern,et al. The role of dynamics in allosteric regulation. , 2003, Current opinion in structural biology.
[40] Jeffrey J. Gray,et al. Contact rearrangements form coupled networks from local motions in allosteric proteins , 2008, Proteins.
[41] Zheng Yang,et al. Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL , 2009, PLoS Comput. Biol..
[42] Phillip Bonacich,et al. Simultaneous group and individual centralities , 1991 .
[43] M. Babu,et al. Molecular signatures of G-protein-coupled receptors , 2013, Nature.
[44] Andrzej Kolinski,et al. Switch from thermal to force-driven pathways of protein refolding. , 2017, The Journal of chemical physics.
[45] S. Takada,et al. Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins , 2011, Proceedings of the National Academy of Sciences.
[46] Andrzej Kolinski,et al. Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model. , 2014, Methods in molecular biology.
[47] Adilson E Motter,et al. Heterogeneity in oscillator networks: are smaller worlds easier to synchronize? , 2003, Physical review letters.
[48] S. Wuchty. Scale-free behavior in protein domain networks. , 2001, Molecular biology and evolution.
[49] Andrej Sali,et al. Structure-based model of allostery predicts coupling between distant sites , 2012, Proceedings of the National Academy of Sciences.
[50] J. Reichardt,et al. Statistical mechanics of community detection. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.
[51] Z. Nevin Gerek,et al. Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning , 2011, PLoS Comput. Biol..
[52] Mauricio Barahona,et al. Synchronization in small-world systems. , 2002, Physical review letters.
[53] C. Sander,et al. Direct-coupling analysis of residue coevolution captures native contacts across many protein families , 2011, Proceedings of the National Academy of Sciences.
[54] Pietro Liò,et al. Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms , 2008, PLoS Comput. Biol..
[55] M. Cieplak,et al. Non-local effects of point mutations on the stability of a protein module. , 2017, The Journal of chemical physics.
[56] Andrzej Kloczkowski,et al. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. , 2018, The Journal of chemical physics.
[57] Andrzej Kolinski,et al. CABS-flex: server for fast simulation of protein structure fluctuations , 2013, Nucleic Acids Res..
[58] Adam Liwo,et al. Protein-folding dynamics: overview of molecular simulation techniques. , 2007, Annual review of physical chemistry.
[59] Weitao Sun,et al. From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact Estimation , 2011, PloS one.
[60] Modesto Orozco,et al. Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field. , 2013, Journal of chemical theory and computation.
[61] Daisuke Kihara,et al. Threading without optimizing weighting factors for scoring function , 2008, Proteins.
[62] R. Nussinov,et al. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. , 2016, Chemical reviews.
[63] Huan‐Xiang Zhou,et al. Protein Allostery and Conformational Dynamics. , 2016, Chemical reviews.
[64] M Karplus,et al. Small-world view of the amino acids that play a key role in protein folding. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.
[65] N. Buchete,et al. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. , 2015, Chemical reviews.
[66] J. Schellman,et al. The Factors Affecting the Stability of Hydrogen-bonded Polypeptide Structures in Solution , 1958 .
[67] Andrzej Kloczkowski,et al. A global machine learning based scoring function for protein structure prediction , 2014, Proteins.
[68] Andrzej Kloczkowski,et al. Four‐body contact potentials derived from two protein datasets to discriminate native structures from decoys , 2007, Proteins.
[69] A. del Sol,et al. Small‐world network approach to identify key residues in protein–protein interaction , 2004, Proteins.
[70] Dahlia R. Weiss,et al. Can morphing methods predict intermediate structures? , 2009, Journal of molecular biology.
[71] J. Changeux,et al. Allosteric Mechanisms of Signal Transduction , 2005, Science.
[72] A. Kloczkowski,et al. A topological order parameter for describing folding free energy landscapes of proteins. , 2018, The Journal of chemical physics.
[73] P Willett,et al. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. , 1993, Journal of molecular biology.
[74] Anirban Banerji,et al. An attempt to construct a (general) mathematical framework to model biological “context-dependence” , 2013, Systems and Synthetic Biology.
[75] R. Nussinov,et al. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM , 2011, Nature Protocols.
[76] L F Lago-Fernández,et al. Fast response and temporal coherent oscillations in small-world networks. , 1999, Physical review letters.
[77] M. Friedman. The Use of Ranks to Avoid the Assumption of Normality Implicit in the Analysis of Variance , 1937 .
[78] Andrzej Kloczkowski,et al. BioShell-Threading: versatile Monte Carlo package for protein 3D threading , 2014, BMC Bioinformatics.
[79] A. Kolinski,et al. Coarse-Grained Protein Models and Their Applications. , 2016, Chemical reviews.
[80] Duncan J. Watts,et al. Collective dynamics of ‘small-world’ networks , 1998, Nature.
[81] Albert,et al. Emergence of scaling in random networks , 1999, Science.
[82] H. Akaike. A new look at the statistical model identification , 1974 .
[83] Dominik Gront,et al. From coarse-grained to atomic-level characterization of protein dynamics: transition state for the folding of B domain of protein A. , 2012, The journal of physical chemistry. B.
[84] Generalized spring tensor models for protein fluctuation dynamics and conformation changes , 2009, BIBM 2009.
[85] R. Jernigan,et al. The energy profiles of atomic conformational transition intermediates of adenylate kinase , 2009, Proteins.
[86] C. Chennubhotla,et al. Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. , 2007, Current opinion in structural biology.
[87] D. Leitner. Energy flow in proteins. , 2008, Annual review of physical chemistry.
[88] Thomas Lengauer,et al. An Algorithm for Finding Maximal Common Subtopologies in a Set of Protein Structures , 1996, J. Comput. Biol..
[89] A. Barabasi,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[90] Douglas L. Theobald,et al. Optimal simultaneous superpositioning of multiple structures with missing data , 2012, Bioinform..
[91] Andrzej Kloczkowski,et al. Deciphering General Characteristics of Residues Constituting Allosteric Communication Paths , 2019, IWBBIO.
[92] R. Nussinov,et al. Conformational ensembles, signal transduction and residue hot spots: application to drug discovery. , 2010, Current opinion in drug discovery & development.
[93] A. Kolinski. Protein modeling and structure prediction with a reduced representation. , 2004, Acta biochimica Polonica.
[94] Chris Smith,et al. Molecular Biology of the Cell (Fifth Edition) , 2008 .
[95] André A. S. T. Ribeiro,et al. A Chemical Perspective on Allostery. , 2016, Chemical reviews.
[96] J. I. Sulkowska,et al. Predicting the order in which contacts are broken during single molecule protein stretching experiments , 2008, Proteins.
[97] A. Kolinski,et al. Structural features that predict real‐value fluctuations of globular proteins , 2012, Proteins.
[98] Dominik Gront,et al. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics , 2013, International journal of molecular sciences.
[99] Andrzej Kloczkowski,et al. Packing regularities in biological structures relate to their dynamics. , 2007, Methods in molecular biology.
[100] Victoria A. Higman,et al. Uncovering network systems within protein structures. , 2003, Journal of molecular biology.
[101] Andrzej Kolinski,et al. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models. , 2015, The Journal of chemical physics.
[102] Aleksandra E. Badaczewska-Dawid,et al. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models , 2018, International journal of molecular sciences.
[103] A. Banerji,et al. A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in proteins , 2009, European Biophysics Journal.
[104] Andrzej Kloczkowski,et al. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes , 2018, Molecules.
[105] J. J. McGregor,et al. Backtrack search algorithms and the maximal common subgraph problem , 1982, Softw. Pract. Exp..
[106] Andrzej Kloczkowski,et al. Classification of Allostery in Proteins: A Deep Learning Approach , 2018 .
[107] Shuai Li,et al. ASD v2.0: updated content and novel features focusing on allosteric regulation , 2013, Nucleic Acids Res..
[108] A. Atilgan,et al. Small-world communication of residues and significance for protein dynamics. , 2003, Biophysical journal.
[109] Aron W Fenton,et al. Allostery: an illustrated definition for the 'second secret of life'. , 2008, Trends in biochemical sciences.
[110] D. Thirumalai,et al. Determination of network of residues that regulate allostery in protein families using sequence analysis , 2006, Protein science : a publication of the Protein Society.
[111] C. Frieden. Kinetic Aspects of Regulation of Metabolic Processes , 2003 .
[112] Dror Tobi,et al. Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition. , 2003, Journal of molecular biology.