Characteristics Analyses and Comparisons of the Protein Structure Networks Constructed by Different Methods

[1]  Nathalie Reuter,et al.  Comparing the intrinsic dynamics of multiple protein structures using elastic network models. , 2015, Biochimica et biophysica acta.

[2]  Jacqueline M. Gulbis,et al.  The molecules of life: physical and chemical principles , 2014 .

[3]  Matteo Tiberti,et al.  PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins , 2014, J. Chem. Inf. Model..

[4]  Daniele Santoni,et al.  Modules Identification in Protein Structures: The Topological and Geometrical Solutions , 2014, J. Chem. Inf. Model..

[5]  Zachary A. Szpiech,et al.  High-resolution network biology: connecting sequence with function , 2013, Nature Reviews Genetics.

[6]  Baofeng Lian,et al.  Site selectivity for protein tyrosine nitration: insights from features of structure and topological network. , 2013, Molecular bioSystems.

[7]  A. Emili,et al.  Protein-protein interaction networks: probing disease mechanisms using model systems , 2013, Genome Medicine.

[8]  A. Giuliani,et al.  Protein contact networks: an emerging paradigm in chemistry. , 2013, Chemical reviews.

[9]  Bairong Shen,et al.  The topology and dynamics of protein complexes: insights from intra- molecular network theory. , 2013, Current protein & peptide science.

[10]  Neil R. Taylor,et al.  Small world network strategies for studying protein structures and binding , 2013, Computational and structural biotechnology journal.

[11]  Ali Rana Atilgan,et al.  Local motifs in proteins combine to generate global functional moves. , 2012, Briefings in functional genomics.

[12]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[13]  Nadezhda T. Doncheva,et al.  Topological analysis and interactive visualization of biological networks and protein structures , 2012, Nature Protocols.

[14]  Sumudu P. Leelananda,et al.  Exploration of the relationship between topology and designability of conformations. , 2011, The Journal of chemical physics.

[15]  Weitao Sun,et al.  From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact Estimation , 2011, PloS one.

[16]  Daniel V. Veres,et al.  Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review , 2011 .

[17]  Saraswathi Vishveshwara,et al.  Interaction energy based protein structure networks. , 2010, Biophysical journal.

[18]  Cristina Marino Buslje,et al.  Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification , 2010, PLoS Comput. Biol..

[19]  S. Vishveshwara,et al.  Intra and inter-molecular communications through protein structure network. , 2009, Current protein & peptide science.

[20]  P. Csermely.  Creative elements: network-based predictions of active centres in proteins and cellular and social networks. , 2008, Trends in biochemical sciences.

[21]  Jianpeng Ma,et al.  OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. , 2008, Journal of molecular biology.

[22]  Masaru Tomita,et al.  Proteins as networks: usefulness of graph theory in protein science. , 2008, Current protein & peptide science.

[23]  Minoru Kanehisa,et al.  AAindex: amino acid index database, progress report 2008 , 2007, Nucleic Acids Res..

[24]  R. Nussinov,et al.  Danger in the dust. , 1996, Genome Biology.

[25]  Csaba Böde,et al.  Network analysis of protein dynamics , 2007, FEBS letters.

[26]  S. Kundu,et al.  Hydrophobic, hydrophilic, and charged amino acid networks within protein. , 2006, Biophysical journal.

[27]  Leonidas J. Guibas,et al.  Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials , 2006, Comput. Aided Geom. Des..

[28]  Michiko Kato,et al.  Systems for the detection and analysis of protein–protein interactions , 2006, Applied Microbiology and Biotechnology.

[29]  S. Vishveshwara,et al.  A network representation of protein structures: implications for protein stability. , 2005, Biophysical journal.

[30]  Oliviero Carugo,et al.  CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures , 2005, Nucleic Acids Res..

[31]  Sudip Kundu,et al.  Amino acid network within protein , 2005 .

[32]  L. Swint-Kruse.  Using networks to identify fine structural differences between functionally distinct protein states. , 2004, Biochemistry.

[33]  Ganesh Bagler,et al.  Network properties of protein structures , 2004, q-bio/0408009.

[34]  Takeshi Kikuchi,et al.  Detection of Pairwise Residue Proximity by Covariation Analysis for 3D-Structure Prediction of G-Protein-Coupled Receptors , 2004, The protein journal.

[35]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[36]  Hongyi Zhou,et al.  Quantifying the effect of burial of amino acid residues on protein stability , 2003, Proteins.

[37]  Victoria A. Higman,et al.  Uncovering network systems within protein structures. , 2003, Journal of molecular biology.

[38]  A. Atilgan,et al.  Small-world communication of residues and significance for protein dynamics. , 2003, Biophysical journal.

[39]  E. Shakhnovich,et al.  Topological determinants of protein folding , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[40]  S. Strogatz.  Exploring complex networks , 2001, Nature.

[41]  S. Vishveshwara,et al.  Identification of side-chain clusters in protein structures by a graph spectral method. , 1999, Journal of molecular biology.

[42]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[43]  C C Bigelow,et al.  On the average hydrophobicity of proteins and the relation between it and protein structure. , 1967, Journal of theoretical biology.

[44]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..