3Drefine: an interactive web server for efficient protein structure refinement

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/.
Source: Nucleic Acids Research - Category: Research Authors: Tags: Web Server issue Source Type: research

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DiscussionMCI prevalence varied among Hispanic/Latino backgrounds, but not as widely as reported in the previous studies. CVD risk and depressive symptoms were associated with increased MCI, whereas APOE4 was not, suggesting alternative etiologies for MCI among diverse Hispanics/Latinos. Our findings suggest that mitigating CVD risk factors may offer important pathways to understanding and reducing MCI and possibly dementia among diverse Hispanics/Latinos.
Source: Alzheimer's and Dementia: The Journal of the Alzheimer's Association - Category: Geriatrics Source Type: research
CONCLUSIONS: Local application of sevoflurane in the wound bed appears to exhibit analgesic, antimicrobial, and positive healing effects. It could be a promising alternative treatment to be included as a therapeutic option for wound care. PMID: 31730517 [PubMed - in process]
Source: Wounds - Category: General Medicine Tags: Wounds Source Type: research
CONCLUSIONS: Cutaneous vasculopathy related to the skin, such as livedo reticularis and ulcers of torpid evolution due to cutaneous vasculopathy are extremely rare. Thus, it is necessary to include skin ulcers as one of the phenotypic manifestations of NF-1. PMID: 31730516 [PubMed - in process]
Source: Wounds - Category: General Medicine Tags: Wounds Source Type: research
CONCLUSIONS: The authors suggest stasis mucinosis and OALM represent the spectrum of euthyroid mucin depositional disease in varying clinical settings. PMID: 31730515 [PubMed - in process]
Source: Wounds - Category: General Medicine Tags: Wounds Source Type: research
CONCLUSIONS: From this case report, the authors believe NPWTi-d may be more effective in cases with intractable ulcers associated with infection that need better granulation. PMID: 31730514 [PubMed - in process]
Source: Wounds - Category: General Medicine Tags: Wounds Source Type: research
Authors: Roshangar L, Soleimani Rad J, Kheirjou R, Reza Ranjkesh M, Ferdowsi Khosroshahi A Abstract Burn wounds are one of the main causes of skin damage. Based on World Health Organization statistics, almost 300 000 people worldwide die of burns each year. In severe burns, the cells and blood vessels are often injured and the blood supply to the wound is disturbed. Many factors such as oxygenation, infection, aging, hormones, and nutrition potentially can influence burn progression and disrupt repair with unbalanced release of various growth factors and cytokines. Different treatment approaches such as dressings a...
Source: Wounds - Category: General Medicine Tags: Wounds Source Type: research
CONCLUSIONS: An illustrated guide for dressing application in burn wounds was developed and validated for content by an expert panel. PMID: 31730512 [PubMed - as supplied by publisher]
Source: Wounds - Category: General Medicine Tags: Wounds Source Type: research
CONCLUSIONS: This is the largest cohort reported in the literature of patients with frostbite injuries treated with HBOT. Hyperbaric oxygen therapy may show positive impact on the demarcation level of frostbite and, despite the common side effects, it generally causes no long-term sequelae. PMID: 31730511 [PubMed - as supplied by publisher]
Source: Wounds - Category: General Medicine Tags: Wounds Source Type: research
CONCLUSIONS: This is an easily reproducible and safe technique for effluent control in patients with Björk grade 4 abdomen with established EAF. PMID: 31730510 [PubMed - as supplied by publisher]
Source: Wounds - Category: General Medicine Tags: Wounds Source Type: research
CONCLUSIONS: These results suggest the importance of arterial-arterial connections such as the pedal arch to the healing potential of foot and ankle wounds after STSG in this high-risk patient population. PMID: 31730509 [PubMed - as supplied by publisher]
Source: Wounds - Category: General Medicine Tags: Wounds Source Type: research
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