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Binding MOAD (Mother Of All Databases)

Liegi Hu, Mark L. Benson, Richard D. Smith, Michael G. Lerner, Heather A. Carlson
2005 Proteins: Structure, Function, and Bioinformatics  
These are based on a statistical potential or knowledge-based approach, which is derived from pairing frequencies of protein-ligand atom pairs observed in a database such as the Protein Data Bank (PDB)  ...  PDB-Ligand PDB-Ligand was designed as a tool to structurally align all of the ligand-binding pockets in the PDB, based on a flexible ligand-clustering method.  ...  A framework is a set of classes and interfaces that are designed to help solve a specific problem and act like a skeleton code for a developer to build upon.  ... 
doi:10.1002/prot.20512 pmid:15971202 fatcat:qya7yxhipzes7ng3dgnc6da4au

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering

Daniel A Keedy, Zachary B Hill, Justin T Biel, Emily Kang, T Justin Rettenmaier, José Brandão-Neto, Nicholas M Pearce, Frank von Delft, James A Wells, James S Fraser
2018 eLife  
New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands.  ...  Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity.  ...  We also 'thank' LK for 'help' with data collection. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.  ... 
doi:10.7554/elife.36307 pmid:29877794 pmcid:PMC6039181 fatcat:z6qukbbp5ne5nfvf2fiyzp4b4i

New routes for PTP1B allosteric inhibition by multitemperature crystallography, fragment screening and covalent tethering [article]

Daniel A Keedy, Zachary B Hill, Justin T Biel, Emily Kang, T. Justin Rettenmaier, Jose Brandao-Neto, Nicholas M Pearce, Frank von Delft, James A. Wells, James S Fraser
2017 bioRxiv   pre-print
Our results converge on a new allosteric site that is conformationally coupled to the active-site WPD loop, a hotspot for fragment binding, not conserved in the closest homolog, and distinct from other  ...  New modeling approaches reveal "hidden" low-occupancy conformational states for protein and ligands.  ...  In 3 of these 82 cases we identified and modeled the ligand from among the possibilities based on the electron density in the event map.  ... 
doi:10.1101/218966 fatcat:bll5xbamebhbtlxn7oq65xa4li

Analysis of the murine granulosa cell transcriptome during luteinisation

Robert Scott McRae
2005
In order to investigate the mechanisms underlying these processes we embarked on a time- and cell-specific analysis of gene expression in the granulosa cell during late follicle development and early luteinisation  ...  The extensive morphological and functional changes which characterise luteinisation involve the regulation of gene and protein expression responsible for the cessation of proliferation and the induction  ...  Initially EST sequencing was one of the most important methods for discovery of novel genes, currently this data is useful in predicting gene coding regions and splice variants from genomic data and for  ... 
doi:10.5525/gla.thesis.71147 fatcat:nkozo3nfarasrnmodj2cw7zuiy