40 research outputs found
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.The workshop was supported by funding to RCSB PDB by the National Science Foundation (DBI 1338415); PDBe by the Wellcome Trust (104948); PDBj by JST-NBDC; BMRB by the National Institute of General Medical Sciences (GM109046); D3R by the National Institute of General Medical Sciences (GM111528); registration fees from industrial participants; and tax-deductible donations to the wwPDB Foundation by the Genentech Foundation and the Bristol-Myers Squibb Foundation.This is the final version of the article. It first appeared from Cell Press via https://doi.org//10.1016/j.str.2016.02.01
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Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.This is the publisher’s final pdf. The published article is copyrighted by Elsevier (Cell Press) and can be found at: http://www.cell.com/structure/hom
Mathematics and Hollywood: A conversation with mathematical Hollywood writers and mathematics faculty
openforcefield/openff-qcsubmit: 0.50.1
<h2>What's Changed</h2>
<ul>
<li>OpenMM to OpenFF units in results/results.py by @chapincavender in https://github.com/openforcefield/openff-qcsubmit/pull/237</li>
<li>Expose ability to set OptimizationProtocols for for optimizations, torsiondrives by @dotsdl in https://github.com/openforcefield/openff-qcsubmit/pull/240</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/openforcefield/openff-qcsubmit/compare/0.50.0...0.50.1</p>
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Advanced Reservoir Characterization in the Antelope Shale to Establish the Viability of CO2 Enhanced Oil Recovery in California's Monterey Formation Siliceous Shales, Class III
The primary objective of this project was to conduct advanced reservoir characterization and modeling studies in the Antelope Shale of the Bureau Vista Hills Field. Work was subdivided into two phases or budget periods. The first phase of the project focused on a variety of advanced reservoir characterization techniques to determine the production characteristics of the Antelope Shale reservoir. Reservoir models based on the results of the characterization work would then be used to evaluate how the reservoir would respond to enhanced oil recovery (EOR) processes such as of CO2 flooding. The second phase of the project would be to implement and evaluate a CO2 in the Buena Vista Hills Field. A successful project would demonstrate the economic viability and widespread applicability of CO2 flooding in siliceous shale reservoirs of the San Joaquin Valley
Fluid Flow Induces Biofilm Formation in Staphylococcus epidermidis Polysaccharide Intracellular Adhesin-Positive Clinical Isolates
Using ORA to explore the relationship of nursing unit communication to patient safety and quality outcomes
The EBEX Balloon-borne Experiment - Gondola, Attitude Control, and Control Software
The E and B Experiment (EBEX) was a long-duration balloon-borne instrument designed to measure the polarization of the cosmic microwave background (CMB) radiation. EBEX was the first balloon-borne instrument to implement a kilopixel array of transition edge sensor (TES) bolometric detectors and the first CMB experiment to use the digital version of the frequency domain multiplexing system for readout of the TES array. The scan strategy relied on 40 s peak-to-peak constant-velocity azimuthal scans. We discuss the unique demands on the design and operation of the payload that resulted from these new technologies and the scan strategy. We describe the solutions implemented, including the development of a power system designed to provide a total of at least 2.3 kW, a cooling system to dissipate 590 W consumed by the detectors' readout system, software to manage and handle the data of the kilopixel array, and specialized attitude reconstruction software. We present flight performance data showing faultless management of the TES array, adequate powering and cooling of the readout electronics, and constraint of attitude reconstruction errors such that the spurious B-modes they induced were less than 10% of the CMB B-mode power spectrum with r = 0.05