98%
921
2 minutes
20
Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008. Both NNcon server and software are available at http://casp.rnet.missouri.edu/nncon.html.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703959 | PMC |
http://dx.doi.org/10.1093/nar/gkp305 | DOI Listing |
Zhongguo Zhong Yao Za Zhi
July 2025
Liaoning University of Traditional Chinese Medicine Shenyang 110847, China Key Laboratory of Ministry of Education for Traditional Chinese Medicine Viscera-State Theory and Applications, Liaoning University of Traditional Chinese Medicine Shenyang 110847, China National and Local Joint Engineering La
This study aimed to investigate the effect and mechanism of Buyang Huanwu Decoction in regulating endoplasmic reticulum stress via the inositol-requiring enzyme 1α(IRE1α)/apoptosis signal-regulating kinase 1(ASK1)/c-Jun N-terminal kinase(JNK) pathway to improve neurological function in rats with cerebral ischemia/reperfusion injury(CIRI). SPF-grade male sprague-dawley(SD) rats were randomly divided into Sham group, model group, Buyang Huanwu Decoction group, and edaravone group. Except for the Sham group, the other groups were subjected to the modified suture method to establish a middle cerebral artery occlusion/reperfusion(MCAO/R) model.
View Article and Find Full Text PDFbioRxiv
August 2025
Department of Chemistry, Western Washington University, Bellingham, WA, USA.
Sortase enzymes are cysteine transpeptidases at the cell surface of gram-positive bacteria. Localized to distinct foci on the cell membrane, class A sortases (SrtAs) recognize a cell wall sorting signal (CWSS), and following cleavage at this specific binding motif, target proteins are ligated to precursors of the growing peptidoglycan layer. This activity of SrtA enzymes is utilized extensively in sortase-mediated ligation (SML) strategies, for a variety of protein engineering applications.
View Article and Find Full Text PDFJ Phys Chem B
September 2025
Department of Physics and Mathematics, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, São Paulo 14800-060, Brazil.
Magnesium ions (Mg) play a crucial role in stabilizing various RNA tertiary motifs, such as pseudoknots, G-quadruplexes, kissing loops, and A-minor motifs, to name a few. Despite their importance, the precise location and role of Mg ions in RNA folding are challenging to characterize both experimentally and computationally. In this study, we employ an all-atom structure-based model integrated with the dynamic counterion condensation (DCC) model to investigate the folding and unfolding transitions of apo SAM-II riboswitch RNA at physiological concentrations of Mg.
View Article and Find Full Text PDFActa Biomater
August 2025
Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, MD, USA. Electronic address:
Tendon mechanical properties are critical for proper musculoskeletal movement. Yet, current understanding of how tendons develop their mechanical properties remains incomplete. Atomic force microscopy and tensile testing are used to characterize early-stage and late-stage embryonic tendon mechanical properties respectively, but both require contact with the tissue, which can alter or destroy tissue structure or integrity and render the tissue unsuitable for subsequent assays.
View Article and Find Full Text PDFJ Food Sci
September 2025
Department of Food safety and quality, Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway.
Cellulose-based materials face limitations in fresh meat packaging applications, which require resistance to moist and fatty foods and high environmental humidity, as well as sufficient gas barrier properties for modified atmosphere packaging (MAP). Even with conventional plastic coating, these materials encounter practical challenges such as sealability and structural stability during storage. This study aimed to evaluate the suitability of recyclable cellulose-based trays coated with polyethylene (PE)/ethylene vinyl alcohol (EVOH)/PE (cellulose/PE/EVOH) for MAP (60% CO/40% N and 75% O/25% CO) of selected fresh foods of animal sources: salmon, chicken, and beef, against polyethylene terephthalate (PET) trays as control.
View Article and Find Full Text PDF