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EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks.
Comput Struct Biotechnol J
December 2024
Department of Computer Science, Virginia Tech, Blacksburg, 24061, VA, USA.
Quality estimation of the predicted interaction interface of protein complex structural models is not only important for complex model evaluation and selection but also useful for protein-protein docking. Despite recent progress fueled by symmetry-aware deep learning architectures and pretrained protein language models (pLMs), existing methods for estimating protein complex quality have yet to fully exploit the collective potentials of these advances for accurate estimation of protein-protein interface. Here we present EquiRank, an improved protein-protein interface quality estimation method by leveraging the strength of a symmetry-aware E(3) equivariant deep graph neural network (EGNN) and integrating pLM embeddings from the pretrained ESM-2 model.
View Article and Find Full Text PDFImpacts of Calculation Grid Spacing and Statistical Uncertainty of Monte Carlo Algorithm on Stereotactic Radiosurgery Planning With Volumetric-Modulated Arcs for Single Brain Metastases Using the Monaco® System.
Cureus
December 2024
Department of Radiology, Aichi Medical University, Nagakute, JPN.
Purpose In linac-based stereotactic radiosurgery (SRS) utilizing a multileaf collimator (MLC) for brain metastases (BMs), a volumetric-modulated arc (VMA) technique is indispensable for generating a suitable dose distribution with efficient planning and delivery. However, the optimal calculation grid spacing (GS) and statistical uncertainty (SU) of the Monte Carlo algorithm for VMA optimization have yet to be determined. This planning study aimed to examine the impacts of GS and GU settings on VMA-based SRS planning and to find the optimal combination for templating.
View Article and Find Full Text PDFSecrets of the Goo: the Genome assembly of the Pacific Banana Slug, Ariolimax columbianus.
J Hered
January 2025
Department of Biomolecular Engineering, University of California, Santa Cruz; Santa Cruz, CA 95064, USA.
The Pacific banana slug, Ariolimax columbianus, is endemic to the forests of the Pacific Northern West. Found throughout coastal foothills and mountains of California, the hermaphroditic molluscs Ariolimax spp. are niche-constrained, hyper-localized, and phenotypically diverse.
View Article and Find Full Text PDFAnalysis of the effect of three different blanching processes on the flavor profile of peeled and unpeeled broad beans.
Food Res Int
February 2025
Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Science, Nanjing 210014, China. Electronic address:
Broad beans, a seasonal leguminous vegetable renowned for their distinctive flavor and high-quality plant protein, present unique opportunities for culinary and nutritional applications. To better understand the impact of various blanching processes on their characteristics, we employed headspace gas chromatography-ion mobility mass spectrometry (HS-GC-IMS) and biochemical tests to evaluate changes in color, volatile compound content, and levels of antioxidant-related substances following different blanching treatments. Our findings revealed that microwave blanching significantly influenced the a* metric and antioxidant capacity of broad beans.
View Article and Find Full Text PDFThe effect of calcium on acute sodium chloride toxicity in Daphnia species.
Environ Toxicol Chem
January 2025
Department of Biology, Queen's University, Kingston, ON, Canada.
Chloride concentrations in freshwater are rising, with toxic effects on aquatic life. In temperate regions with cold winters, road salt used for deicing paved surfaces is a primary cause. There is evidence that water hardness can modify salt toxicity, but data are insufficient to inform policy.
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