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16
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
- Nucleic Acids Res
, 2015
"... The RCSB Protein Data Bank (RCSB PDB, ..."
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The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res
"... biology for basic and applied research and education ..."
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biology for basic and applied research and education
CSAR data set release 2012: ligands, affinities, complexes, and docking
"... ABSTRACT: A major goal in drug design is the improvement of computational methods for docking and scoring. The Community Structure Activity Resource (CSAR) has collected several data sets from industry and added in-house data sets that may be used for this purpose (www.csardock.org). CSAR has curren ..."
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ABSTRACT: A major goal in drug design is the improvement of computational methods for docking and scoring. The Community Structure Activity Resource (CSAR) has collected several data sets from industry and added in-house data sets that may be used for this purpose (www.csardock.org). CSAR has currently obtained data from Abbott, GlaxoSmithKline, and Vertex and is working on obtaining data from several others. Combined with our in-house projects, we are providing a data set consisting of 6 protein targets, 647 compounds with biological affinities, and 82 crystal structures. Multiple congeneric series are available for several targets with a few representative crystal structures of each of the series. These series generally contain a few inactive compounds, usually not available in the literature, to provide an upper bound to the affinity range. The affinity ranges are typically 3−4 orders of magnitude per series. For our in-house projects, we have had compounds synthesized for biological testing. Affinities were measured by Thermofluor, Octet RED, and isothermal titration calorimetry for the most soluble. This allows the direct comparison of the biological affinities for those compounds, providing a measure of the variance in the experimental affinity. It appears that there can be considerable variance in the absolute value of the affinity, making the prediction of the absolute value ill-defined. However, the
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage
- Nucleic Acids Res
, 2014
"... The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed f ..."
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The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ri-bozyme. The results correct local conformations and identify alternates for RNA residues, many in func-tionally important regions, leading to improved R val-ues and model validation statistics for both struc-tures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both in-hibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the bio-chemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and cat-alytic mechanism of the HDV ribozyme and demon-strate the power of new techniques to make signif-icant improvements in RNA structures that impact biologically relevant conclusions.
1 Structural Bioinformatics
"... lDDT: A local superposition-free score for comparing protein structures and models using distance difference tests ..."
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lDDT: A local superposition-free score for comparing protein structures and models using distance difference tests
Using Protein-Likeness to Validate Conformational Alternatives
, 2012
"... ...strating that backrubs also accompany sequence changes and therefore are useful for modeling conformational changes associated with mutations in protein design. Second, I extensively studied a new local backbone motion, helix shear, by documenting its occurrence in both crystal and NMR structures ..."
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...strating that backrubs also accompany sequence changes and therefore are useful for modeling conformational changes associated with mutations in protein design. Second, I extensively studied a new local backbone motion, helix shear, by documenting its occurrence in both crystal and NMR structures and showing its suitability for expanding conformational search space in protein design. Third, I integrated many types of local alternate conformations in an ultra-high-resolution crystal structure and discovered the combinatorial complexity that arises when adjacent flexible segments combine into networks. Fourth, I used structural bioinformatics techniques to construct smoothed, multi-dimensional torsional distributions that can be used to validate trial conformations or to propose new ones. Fifth, I participated in judging a structure prediction competition by using validation of geometrical and all-atom contact criteria to help define correctness across thousands of submitted conformations. Sixth, using similar tools plus collation of multiple comparable structures from the public database, I determined that low-energy states identified by the popular structure modeling suite Rosetta sometimes are valid conformations likely to be populated
Structural bioinformatics Advance access publication August 23, 2010
, 2010
"... OpenStructure: a flexible software framework for computational structural biology ..."
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OpenStructure: a flexible software framework for computational structural biology
Structure Meeting Review Outcome of the First wwPDB Hybrid/Integrative
"... Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDBHybrid/Integrative Methods Task ForceWorkshop held at the European B ..."
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Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDBHybrid/Integrative Methods Task ForceWorkshop held at the European Bioinformatics h v ra s a
structure, dynamics and cleavage
, 2014
"... New tools provide a second look at HDV ribozyme ..."
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