Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities.
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Gary D Bader | Philip M. Kim | J. Min | Shobhit Jain | J. Teyra | S. Sidhu | Y. Tong | A. Dong | Haiming Huang | W. Tempel | X. Guan | Yanli Liu | J. Min
[1] A. Cámara-Artigas,et al. The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase. , 2016, Acta crystallographica. Section F, Structural biology communications.
[2] S. Li,et al. Large-Scale Screening of Preferred Interactions of Human Src Homology-3 (SH3) Domains Using Native Target Proteins as Affinity Ligands* , 2016, Molecular & Cellular Proteomics.
[3] S. Marqusee,et al. When the Scaffold Cannot Be Ignored: The Role of the Hydrophobic Core in Ligand Binding and Specificity. , 2015, Journal of molecular biology.
[4] S. Knapp,et al. Differential Recognition Preferences of the Three Src Homology 3 (SH3) Domains from the Adaptor CD2-associated Protein (CD2AP) and Direct Association with Ras and Rab Interactor 3 (RIN3)* , 2015, The Journal of Biological Chemistry.
[5] C. Quince,et al. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform , 2015, Nucleic acids research.
[6] Hai Fang,et al. The SUPERFAMILY 1.75 database in 2014: a doubling of data , 2014, Nucleic Acids Res..
[7] D. Gfeller,et al. A structural portrait of the PDZ domain family. , 2014, Journal of molecular biology.
[8] Peer Bork,et al. SMART: recent updates, new developments and status in 2015 , 2014, Nucleic Acids Res..
[9] Q. Gong,et al. Structural investigation of the interaction between the tandem SH3 domains of c-Cbl-associated protein and vinculin. , 2014, Journal of structural biology.
[10] W. Schubert,et al. Structural details of human tuba recruitment by InlC of Listeria monocytogenes elucidate bacterial cell-cell spreading. , 2014, Structure.
[11] Dongfang Liu. The adaptor protein Crk in immune response , 2014, Immunology and cell biology.
[12] Ignacio E. Sánchez,et al. The eukaryotic linear motif resource ELM: 10 years and counting , 2013, Nucleic Acids Res..
[13] Philip R. Evans,et al. How good are my data and what is the resolution? , 2013, Acta crystallographica. Section D, Biological crystallography.
[14] Alan Bridge,et al. New and continuing developments at PROSITE , 2012, Nucleic Acids Res..
[15] P. Permi,et al. SH3 domain ligand binding: What's the consensus and where's the specificity? , 2012, FEBS letters.
[16] A. Davidson,et al. Distinct Peptide Binding Specificities of Src Homology 3 (SH3) Protein Domains Can Be Determined by Modulation of Local Energetics across the Binding Interface* , 2012, The Journal of Biological Chemistry.
[17] Gary D. Bader,et al. MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets , 2011, Nucleic acids research.
[18] L. Holm,et al. The Pfam protein families database , 2011, Nucleic Acids Res..
[19] M. Teresa Pisabarro,et al. SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds , 2011, BMC Bioinformatics.
[20] N. Pannu,et al. REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.
[21] Sindy K. Y. Tang,et al. Diversity of Phage-Displayed Libraries of Peptides during Panning and Amplification , 2011, Molecules.
[22] Arnaud Céol,et al. 3did: identification and classification of domain-based interactions of known three-dimensional structure , 2010, Nucleic Acids Res..
[23] Vincent B. Chen,et al. MolProbity: all-atom structure validation for macromolecular crystallography , 2009, Acta crystallographica. Section D, Biological crystallography.
[24] Gary D. Bader,et al. Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins , 2009, PLoS biology.
[25] M. Lewitzky,et al. Distinct binding modes of two epitopes in Gab2 that interact with the SH3C domain of Grb2. , 2009, Structure.
[26] L. Shaw,et al. Cell Communication and Signaling Crk and Crkl Adaptor Proteins: Networks for Physiological and Pathological Signaling , 2009 .
[27] P. Permi,et al. Structural basis of PxxDY motif recognition in SH3 binding. , 2009, Journal of molecular biology.
[28] Chris Sander,et al. A Specificity Map for the PDZ Domain Family , 2008, PLoS biology.
[29] E. Reinherz,et al. Structural and functional evidence that Nck interaction with CD3epsilon regulates T-cell receptor activity. , 2008, Journal of molecular biology.
[30] Tony Pawson,et al. Defining the Specificity Space of the Human Src Homology 2 Domain*S , 2008, Molecular & Cellular Proteomics.
[31] T. Sakmar,et al. A Novel Interaction between Atrophin-interacting Protein 4 and β-p21-activated Kinase-interactive Exchange Factor Is Mediated by an SH3 Domain* , 2007, Journal of Biological Chemistry.
[32] R. Wagner,et al. Reciprocal Regulation of SH3 and SH2 Domain Binding via Tyrosine Phosphorylation of a Common Site in CD3ε1 , 2007, The Journal of Immunology.
[33] Randy J. Read,et al. Phaser crystallographic software , 2007, Journal of applied crystallography.
[34] M. Shipston,et al. A noncanonical SH3 domain binding motif links BK channels to the actin cytoskeleton via the SH3 adapter cortactin , 2006, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[35] Kevin Cowtan,et al. The Buccaneer software for automated model building. 1. Tracing protein chains. , 2006, Acta crystallographica. Section D, Biological crystallography.
[36] Kevin Cowtan,et al. The Buccaneer software for automated model building , 2006 .
[37] A. Hoelz,et al. Crystal structure of the SH3 domain of betaPIX in complex with a high affinity peptide from PAK2. , 2006, Journal of molecular biology.
[38] Thomas Szyperski,et al. A structure-based model of the c-Myc/Bin1 protein interaction shows alternative splicing of Bin1 and c-Myc phosphorylation are key binding determinants. , 2005, Journal of molecular biology.
[39] Rolf Apweiler,et al. InterProScan: protein domains identifier , 2005, Nucleic Acids Res..
[40] Wendell A. Lim,et al. Optimization of specificity in a cellular protein interaction network by negative selection , 2003, Nature.
[41] M. Lewitzky,et al. Structural basis for SH3 domain‐mediated high‐affinity binding between Mona/Gads and SLP‐76 , 2003, The EMBO journal.
[42] T. Pawson,et al. Assembly of Cell Regulatory Systems Through Protein Interaction Domains , 2003, Science.
[43] Tony Pawson,et al. Structural basis for specific binding of the Gads SH3 domain to an RxxK motif-containing SLP-76 peptide: a novel mode of peptide recognition. , 2003, Molecular cell.
[44] Daisuke Kohda,et al. Diverse recognition of non‐PxxP peptide ligands by the SH3 domains from p67phox, Grb2 and Pex13p , 2002, The EMBO journal.
[45] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[46] Gianni Cesareni,et al. Normalization of nomenclature for peptide motifs as ligands of modular protein domains , 2002, FEBS letters.
[47] Gary D Bader,et al. A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules , 2001, Science.
[48] K. Miyazawa,et al. A Deubiquitinating Enzyme UBPY Interacts with the Src Homology 3 Domain of Hrs-binding Protein via a Novel Binding Motif PX(V/I)(D/N)RXXKP* , 2000, The Journal of Biological Chemistry.
[49] T. Pawson,et al. Signaling through scaffold, anchoring, and adaptor proteins. , 1997, Science.
[50] V S Lamzin,et al. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models. , 1997, Acta crystallographica. Section D, Biological crystallography.
[51] Dan Gusfield,et al. Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .
[52] B. Chait,et al. Crystal Structure of the Conserved Core of HIV-1 Nef Complexed with a Src Family SH3 Domain , 1996, Cell.
[53] Wendell A. Lim,et al. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains , 1995, Nature.
[54] S. Schreiber,et al. Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. , 1995, Science.
[55] A. Sali,et al. Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk. , 1995, Structure.
[56] M. Saraste,et al. Backwards and forwards binding , 1994, Nature Structural Biology.
[57] Andrea Musacchio,et al. High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides , 1994, Nature Structural Biology.
[58] Hongtao Yu,et al. Structural basis for the binding of proline-rich peptides to SH3 domains , 1994, Cell.
[59] P Cicchetti,et al. Identification of a ten-amino acid proline-rich SH3 binding site. , 1993, Science.
[60] D. Baltimore,et al. Identification of a protein that binds to the SH3 region of Abl and is similar to Bcr and GAP-rho. , 1992, Science.
[61] T. D. Schneider,et al. Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.
[62] Gary D Bader,et al. SH3 interactome conserves general function over specific form , 2013, Molecular systems biology.
[63] Sachdev S Sidhu,et al. Engineering and analysis of peptide-recognition domain specificities by phage display and deep sequencing. , 2013, Methods in enzymology.
[64] Livia Perfetto,et al. The protein interaction network mediated by human SH3 domains. , 2012, Biotechnology advances.
[65] Gary D Bader,et al. The multiple-specificity landscape of modular peptide recognition domains , 2011, Molecular systems biology.
[66] Sachdev S Sidhu,et al. Studying binding specificities of peptide recognition modules by high-throughput phage display selections. , 2011, Methods in molecular biology.
[67] Alexei Vagin,et al. Molecular replacement with MOLREP. , 2010, Acta crystallographica. Section D, Biological crystallography.
[68] P. Emsley,et al. Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.
[69] Serge X. Cohen,et al. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 , 2008, Nature Protocols.
[70] Raffi Tonikian,et al. Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries , 2007, Nature Protocols.
[71] James E. Bray,et al. The CATH database: an extended protein family resource for structural and functional genomics , 2003, Nucleic Acids Res..
[72] Stefan M. Larson,et al. The identification of conserved interactions within the SH3 domain by alignment of sequences and structures , 2000, Protein science : a publication of the Protein Society.
[73] B. Mayer,et al. Functions of SH2 and SH3 domains. , 1998, Current topics in microbiology and immunology.
[74] D Cowburn,et al. Modular peptide recognition domains in eukaryotic signaling. , 1997, Annual review of biophysics and biomolecular structure.
[75] Z. Otwinowski,et al. [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.