Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments
暂无分享,去创建一个
Juan Fernández-Recio | Patrick Aloy | Roberto Mosca | Carles Pons | P. Aloy | J. Fernández-Recio | Roberto Mosca | Carles Pons
[1] Brian E Snydsman,et al. Assigning function to yeast proteins by integration of technologies. , 2003, Molecular cell.
[2] Carlos J Camacho,et al. Successful discrimination of protein interactions , 2003, Proteins.
[3] Jeffrey J. Gray,et al. High-resolution protein-protein docking. , 2006, Current opinion in structural biology.
[4] Solène Grosdidier,et al. Prediction and scoring of docking poses with pyDock , 2007, Proteins.
[5] Gary D Bader,et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.
[6] E. Katchalski‐Katzir,et al. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[7] R. Abagyan,et al. Soft protein–protein docking in internal coordinates , 2002, Protein science : a publication of the Protein Society.
[8] Z. Weng,et al. ZDOCK: An initial‐stage protein‐docking algorithm , 2003, Proteins.
[9] M. Sternberg,et al. Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.
[10] James R. Knight,et al. A Protein Interaction Map of Drosophila melanogaster , 2003, Science.
[11] Ruth Nussinov,et al. Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.
[12] Marc A. Martí-Renom,et al. MODBASE: a database of annotated comparative protein structure models and associated resources , 2005, Nucleic Acids Res..
[13] Roberto Mosca,et al. Alignment of protein structures in the presence of domain motions , 2008, BMC Bioinformatics.
[14] Hans-Werner Mewes,et al. MPact: the MIPS protein interaction resource on yeast , 2005, Nucleic Acids Res..
[15] A. Barabasi,et al. High-Quality Binary Protein Interaction Map of the Yeast Interactome Network , 2008, Science.
[16] S. L. Wong,et al. A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.
[17] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[18] C. DeLisi,et al. Determination of atomic desolvation energies from the structures of crystallized proteins. , 1997, Journal of molecular biology.
[19] Zhiping Weng,et al. Docking unbound proteins using shape complementarity, desolvation, and electrostatics , 2002, Proteins.
[20] C. Camacho,et al. Modeling side‐chains using molecular dynamics improve recognition of binding region in CAPRI targets , 2005, Proteins.
[21] A. Lesk,et al. The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.
[22] S. L. Wong,et al. Towards a proteome-scale map of the human protein–protein interaction network , 2005, Nature.
[23] C. Dominguez,et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.
[24] Sean R. Collins,et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.
[25] James R. Knight,et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.
[26] D. Ritchie,et al. Protein docking using spherical polar Fourier correlations , 2000, Proteins.
[27] Narayanan Eswar,et al. Protein structure modeling with MODELLER. , 2008, Methods in molecular biology.
[28] P. Bork,et al. Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.
[29] Sandor Vajda,et al. Classification of protein complexes based on docking difficulty , 2005, Proteins.
[30] T. Hughes,et al. High-definition macromolecular composition of yeast RNA-processing complexes. , 2004, Molecular cell.
[31] Z. Weng,et al. Integrating statistical pair potentials into protein complex prediction , 2007, Proteins.
[32] S. Vajda,et al. Protein-protein docking: is the glass half-full or half-empty? , 2004, Trends in biotechnology.
[33] Patrick Aloy,et al. Incorporating high‐throughput proteomics experiments into structural biology pipelines: Identification of the low‐hanging fruits , 2008, Proteomics.
[34] Tammy M. K. Cheng,et al. pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking , 2007, Proteins.
[35] Gianni Cesareni,et al. WI‐PHI: A weighted yeast interactome enriched for direct physical interactions , 2007, Proteomics.
[36] Martin Vingron,et al. IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..
[37] Z. Weng,et al. Protein–protein docking benchmark version 3.0 , 2008, Proteins.
[38] Arun K. Ramani,et al. How complete are current yeast and human protein-interaction networks? , 2006, Genome Biology.
[39] Adrian A Canutescu,et al. A graph‐theory algorithm for rapid protein side‐chain prediction , 2003, Protein science : a publication of the Protein Society.
[40] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[41] Gabriele Ausiello,et al. MINT: the Molecular INTeraction database , 2006, Nucleic Acids Res..
[42] Patrick Aloy,et al. Contextual Specificity in Peptide-Mediated Protein Interactions , 2008, PloS one.
[43] Z. Weng,et al. A novel shape complementarity scoring function for protein‐protein docking , 2003, Proteins.
[44] Z. Weng,et al. Optimizing protein representations with information theory. , 2004, Genome informatics. International Conference on Genome Informatics.
[45] R. Russell,et al. The relationship between sequence and interaction divergence in proteins. , 2003, Journal of molecular biology.
[46] David W Ritchie,et al. Recent progress and future directions in protein-protein docking. , 2008, Current protein & peptide science.
[47] P. Bork,et al. Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.
[48] S. Wodak,et al. Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures , 2005, Proteins.
[49] Alexandre M J J Bonvin,et al. Flexible protein-protein docking. , 2006, Current opinion in structural biology.
[50] Jeffrey J. Gray,et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. , 2003, Journal of molecular biology.
[51] P. Bork,et al. Structure-Based Assembly of Protein Complexes in Yeast , 2004, Science.
[52] Miriam Eisenstein,et al. Inherent limitations in protein-protein docking procedures , 2007, Bioinform..
[53] S. Wodak,et al. Docking and scoring protein complexes: CAPRI 3rd Edition , 2007, Proteins.
[54] R. Abagyan,et al. ICM‐DISCO docking by global energy optimization with fully flexible side‐chains , 2003, Proteins.
[55] Martin Zacharias,et al. ATTRACT: Protein–protein docking in CAPRI using a reduced protein model , 2005, Proteins.
[56] R. Ozawa,et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[57] R. Russell,et al. Targeting and tinkering with interaction networks. , 2008, Nature chemical biology.
[58] David Botstein,et al. SGD: Saccharomyces Genome Database , 1998, Nucleic Acids Res..
[59] H. Lehrach,et al. A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome , 2005, Cell.
[60] Patrick Aloy,et al. Ten thousand interactions for the molecular biologist , 2004, Nature Biotechnology.
[61] Maxim Totrov,et al. Improving CAPRI predictions: Optimized desolvation for rigid‐body docking , 2005, Proteins.
[62] Zhiping Weng,et al. Protein–protein docking benchmark version 4.0 , 2010, Proteins.
[63] S. Wodak,et al. Assessment of blind predictions of protein–protein interactions: Current status of docking methods , 2003, Proteins.