AI Article Synopsis
- Deformable elastic network (DEN) restraints help improve the accuracy of structure refinement from low-resolution X-ray data but require significant computational power.
- The new DEN web service allows structural biologists to leverage the Open Science Grid for faster and more efficient DEN refinements through an easy-to-use interface in the SBGrid Science Portal.
- An example showcasing the use of DEN restraints on the human Notch1 transcriptional complex demonstrates the effectiveness of this web service, highlighting its ability to reduce processing time from thousands of hours to just a few.
Article Abstract
Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282622 | PMC |
| http://dx.doi.org/10.1107/S0907444912001163 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
[Effects of the Decision of the German Constitutional Court on mechanical restraint in 2018 : Coercive measures in the psychiatric hospitals in Baden-Wuerttemberg in 2019 compared to the years 2015-2017].
Nervenarzt
July 2022
Klinik für Psychiatrie und Psychotherapie I, Universität Ulm (Weissenau), Ravensburg, Deutschland.
On 23 July 2018 the German Constitutional Court decided that mechanical restraint in psychiatric patients with 5 or 7‑point mechanical restraint lasting longer than 30 min requires a judicial authorization. On the same day, the German Association for Psychiatry and Psychotherapy (DGPPN) published guidelines on the prevention of coercion and violence. Together, this can be considered as the strongest intervention to reduce coercion on a national level worldwide.
View Article and Find Full Text PDFUtility of a Structured Teaching Approach, Rehearsal, and Training for Patients With Autism Spectrum Disorder to Avoid Physical Restraint During Induction of Anesthesia.
J Perianesth Nurs
April 2022
Department of Dental Anesthesiology, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan.
Purpose: We aimed to determine whether the use of a structured teaching approach, rehearsing, and training (SRT) for anesthesia induction in patients with autism spectrum disorder (ASD) could reduce the need for physical restraint.
Design: Retrospective observational study METHODS: We retrospectively analyzed 63 patients (4 to 40 y old) with ASD who underwent general anesthesia for dental treatment. Patients were divided into SRT (n = 22) and non-SRT (n = 41) groups.
Improving sampling of crystallographic disorder in ensemble refinement.
Acta Crystallogr D Struct Biol
November 2021
Chemistry and Pharmaceutical Sciences, Free University of Amsterdam, Amsterdam, The Netherlands.
Ensemble refinement, the application of molecular dynamics to crystallographic refinement, explicitly models the disorder inherent in macromolecular structures. These ensemble models have been shown to produce more accurate structures than traditional single-model structures. However, suboptimal sampling of the molecular-dynamics simulation and modelling of crystallographic disorder has limited the utility of the method, and can lead to unphysical and strained models.
View Article and Find Full Text PDFMicellization of Sequence-Controlled Polyurethane Ionomers in Mixed Aqueous Solvents.
Macromolecules
March 2021
Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands.
While the impact of compositional parameters such as block length and ionic content on the micellization of (polymeric) amphiphiles is widely investigated, the influence of monomer sequence has received far less attention until recently. Here, we report the synthesis of two sequence-controlled polyurethane ionomers (PUIs) prepared via a stepwise coupling-deprotection strategy, and compare their solution association in aqueous-organic mixtures. The two PUIs are highly similar in mass and overall composition, yet differ markedly in the sequence of building blocks.
View Article and Find Full Text PDF[Clinical ethic consultations in longterm care in Upper Austria-5 years report of the Landesverband Hospiz Upper Austria].
Wien Med Wochenschr
May 2022
Landesverband Hospiz, Pfalzgasse 2, 4055, Pupping, Österreich.
Despite the unique nature of ethical issues in a longterm care setting, there is limited help in decision making for nursing home personnel. 2015 the Hospizverband of Upper Austria established a clinical ethic committee to help providing a good quality of decision making in nursing home. A consultation could be asked by the managing nurses of the longterm care institution, by the resident or by relatives of the nursing home residents.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!