Prediction of Functional Sites in SCOP Domains using Dynamics Perturbation Analysis

Judith D. Cohn, Dengming Ming, Michael E. Wall* Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, 87545 USA Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545 USA Center for Non-Linear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210093, People's Republic of China *To whom correspondence should be addressed: mewall@lanl.gov

[1]  J A Eisen,et al.  Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. , 1998, Genome research.

[2]  M. Wall,et al.  Allostery in a coarse-grained model of protein dynamics. , 2005, Physical review letters.

[3]  Kui Zhang,et al.  Prediction of protein function using protein-protein interaction data , 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

[4]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[5]  Janet M Thornton,et al.  Protein function prediction using local 3D templates. , 2005, Journal of molecular biology.

[6]  Jan Freudenberg,et al.  A similarity-based method for genome-wide prediction of disease-relevant human genes , 2002, ECCB.

[7]  Daisuke Kihara,et al.  Enhanced automated function prediction using distantly related sequences and contextual association by PFP , 2006, Protein science : a publication of the Protein Society.

[8]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[9]  Limsoon Wong,et al.  Exploiting indirect neighbours and topological weight to predict protein function from protein--protein interactions , 2006 .

[10]  B. Rost,et al.  Automatic prediction of protein function , 2003, Cellular and Molecular Life Sciences CMLS.

[11]  Carl J. Schmidt,et al.  GoFigure: Automated Gene OntologyTM annotation , 2003, Bioinform..

[12]  B. Snel,et al.  Predicting disease genes using protein–protein interactions , 2006, Journal of Medical Genetics.

[13]  Søren Brunak,et al.  Prediction of human protein function according to Gene Ontology categories , 2003, Bioinform..

[14]  Miguel A. Andrade-Navarro,et al.  Automated genome sequence analysis and annotation , 1999, Bioinform..

[15]  Janet M. Thornton,et al.  ProFunc: a server for predicting protein function from 3D structure , 2005, Nucleic Acids Res..

[16]  Karin M. Verspoor,et al.  A categorization approach to automated ontological function annotation , 2006, Protein science : a publication of the Protein Society.

[17]  Andreas Herrmann,et al.  Bilayer conformation of fusion peptide of influenza virus hemagglutinin: a molecular dynamics simulation study. , 2004, Biophysical journal.

[18]  Benoît Roux,et al.  Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids. , 2005, Journal of molecular biology.

[19]  M Karplus,et al.  The fundamentals of protein folding: bringing together theory and experiment. , 1999, Current opinion in structural biology.

[20]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[21]  Luca Benini,et al.  TOM: a web-based integrated approach for identification of candidate disease genes , 2006, Nucleic Acids Res..

[22]  Judith D. Cohn,et al.  Fast dynamics perturbation analysis for prediction of protein functional sites , 2008, BMC Structural Biology.

[23]  Peter M. Kasson,et al.  Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide , 2006, Pacific Symposium on Biocomputing.

[24]  C. Dobson.  The structural basis of protein folding and its links with human disease. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[25]  M. Fisher,et al.  Proline to the rescue , 2006, Proceedings of the National Academy of Sciences.

[26]  Pall I. Olason,et al.  A human phenome-interactome network of protein complexes implicated in genetic disorders , 2007, Nature Biotechnology.

[27]  Arvi Rauk,et al.  Molecular dynamics study of the beta amyloid peptide of Alzheimer's disease and its divalent copper complexes. , 2007, The journal of physical chemistry. B.

[28]  M. Wall,et al.  Quantifying allosteric effects in proteins , 2005, Proteins.

[29]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[30]  Hans Lehrach,et al.  GOblet: a platform for Gene Ontology annotation of anonymous sequence data , 2004, Nucleic Acids Res..

[31]  M. Wall,et al.  Interactions in native binding sites cause a large change in protein dynamics. , 2006, Journal of molecular biology.

[32]  Eleazar Eskin,et al.  The Spectrum Kernel: A String Kernel for SVM Protein Classification , 2001, Pacific Symposium on Biocomputing.

[33]  Janet M. Thornton,et al.  The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data , 2004, Nucleic Acids Res..

[34]  C. A. Andersen,et al.  Prediction of human protein function from post-translational modifications and localization features. , 2002, Journal of molecular biology.

[35]  Frances S. Turner,et al.  POCUS: mining genomic sequence annotation to predict disease genes , 2003, Genome Biology.

[36]  Jason Y. Liu,et al.  Analysis of protein sequence and interaction data for candidate disease gene prediction , 2006, Nucleic acids research.

[37]  Russ B. Altman,et al.  Recognizing Complex, Asymmetric Functional Sites in Protein Structures Using a Bayesian Scoring Function , 2003, J. Bioinform. Comput. Biol..

[38]  M. S. Shamsir,et al.  One gene, two diseases and three conformations: Molecular dynamics simulations of mutants of human prion protein at room temperature and elevated temperatures , 2005, Proteins.

[39]  Michael Y. Galperin,et al.  Beyond complete genomes: from sequence to structure and function. , 1998, Current opinion in structural biology.

[40]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[41]  Yves A. Lussier,et al.  An integrative model for in-silico clinical-genomics discovery science , 2002, AMIA.

[42]  P. Dobson,et al.  Predicting enzyme class from protein structure without alignments. , 2005, Journal of molecular biology.

[43]  Michael I. Jordan,et al.  Protein Molecular Function Prediction by Bayesian Phylogenomics , 2005, PLoS Comput. Biol..

[44]  Y. Freund,et al.  Profile-based string kernels for remote homology detection and motif extraction. , 2005, Journal of bioinformatics and computational biology.

[45]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[46]  M. Sternberg,et al.  Automated prediction of protein function and detection of functional sites from structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Chris Sander,et al.  The HSSP data base of protein structure-sequence alignments , 1993, Nucleic Acids Res..

[48]  Chitta Baral,et al.  Mining gene-disease relationships from biomedical literature: weighting protein-protein interactions and connectivity measures. , 2006, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[49]  P. Bork,et al.  Association of genes to genetically inherited diseases using data mining , 2002, Nature Genetics.

[50]  M A Andrade,et al.  Bioinformatics: from genome data to biological knowledge. , 1997, Current opinion in biotechnology.

[51]  C. Sander,et al.  A method to predict functional residues in proteins , 1995, Nature Structural Biology.

[52]  Geoffrey J. Barton,et al.  The Jalview Java alignment editor , 2004, Bioinform..

[53]  Tijl De Bie,et al.  Kernel-based data fusion for gene prioritization , 2007, ISMB/ECCB.

[54]  C. Wijmenga,et al.  Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. , 2006, American journal of human genetics.

[55]  P. Radivojac,et al.  An integrated approach to inferring gene–disease associations in humans , 2008, Proteins.

[56]  Geoffrey J. Barton,et al.  GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes , 2004, BMC Bioinformatics.