Deep-learning models have transformed our ability to predict the phenotypic effects of sequence perturbations. Protein language models (pLMs) score the evolutionary propensity of any amino-acid substitution, emerging as fast and accurate predictors of fitness changes. Inverse-folding (IF) models add structural informat...
Ezequiel A. Galpern, Charles W. J. Pugh, Mafalda Dias et al.· ChemRxiv· 0 citations
The phosphoinositide 3-kinase (PI3K)/3-phosphoinositide-dependent protein kinase-1 (PDK1)/protein kinase B (AKT) signaling axis is dysregulated in breast cancer progression and therapeutic resistance. In this study, an integrated computational workflow was developed to prioritize FDA-approved drugs as potential PDK1-ta...
НА РУССКОМ (RU): Аннотация. Завершающая работа трилогии PANCHONDRIOME 3.5 переходит от макроскопических метафор к квантово-полевому базису живой материи — голограмме Фрёлиха, выводя пространственный инвариант морфогенеза dL = 6.25 мкм на стыке ТГц Бозе-конденсации (0.24 ТГц) и EZ-воды Поллака. Представлено опровержение...
Konstantin D. Pisarenko· Zenodo (CERN European Organi...· 0 citations
This dataset provides the source-data files underlying the figures and the reagent inventories of the study "Aqueous Hellenia speciosa rhizome extract attenuates hepatic injury in high-fat diet/streptozotocin-induced diabetic rats" (Filfilan & Elbeeh). Included: (1) Figure 6 per-field morphometric source values (steato...
Background: Amazonian biodiversity includes plant resources with potential metabolic activity. Buriti (Mauritia flexuosa) contains monounsaturated fatty acids, carotenoids, and phenolic compounds. Objectives: This study evaluated treatment-associated biochemical and morphological differences after buriti oil or lyophil...
Final reproducibility package aligned with the train-fold-only PCA development analysis, within-benchmark antifungal confirmation, external TAPE remote-homology validation, Supplementary Tables S1-S6 and current Figure 1-3 source data.
renxingye110· Zenodo (CERN European Organi...· 0 citations
Structural analysis and fluorometric evidence indicate that, over evolutionary time, these proteins lost the ability to properly bind GSSG, thereby abolishing hyper-reactivity, and pKa values of their cysteines are scattered across a wide range, resulting in a hierarchical reactivity toward GSSG that may be crucial for...
Unknown authors· Biochemical and Biophysical...· 0 citations
This work probes the structure and function of the orphan toxin-immunity pair Rhs2-SciX, demonstrates the biochemical diversity of Salmonella T6SS effectors, and highlights the conserved T6SS toxicity strategy of binding EF-Tu.
N. Cobo, S. Goyal, David E. Davidson et al.· Journal of Molecular Biology· 0 citations
Intramolecular distances existing between the sheets that define the β-barrel fold of BsCspB have been shown to respond nonuniformly to increasing hydrostatic pressure, suggesting that the three-dimensional structure of native BsCspB is modified such that β-strands depart from each other.
Frédéric Berner, Michael Kovermann· Biophysical Journal· 0 citations
Abstract Metabolite abundances represent the ultimate functional outputs of cellular processes and provide a direct link between genotype and phenotype. While the evolutionary dynamics of mRNA and protein abundances have been extensively studied, the evolutionary forces shaping metabolite abundances remain largely unex...
Hai-Chao Li, Hao-Xuan Liu· Molecular biology and evolut...· 0 citations
It is demonstrated that PPARα exerts a protective effect against RVH, at least in part, by promoting fatty acid oxidation through upregulation of its downstream target proteins CPT-1 and acyl-CoA oxidase 1.
Xiao-Ying Zhang, Jia-Jia Wu, Yu-Chan Zhang et al.· High Altitude Medicine & Bio...· 0 citations
Side chain assignments are essential for in-depth characterization of proteins. We present here two refined TOCSY experiments based on the use of a variant of “perfect echo” to partially suppress the negative effects arising from homonuclear 13C couplings in the indirect dimension: The iPE-(H)CCH-TOCSY for correlating...
Arnelle Löbbert, Aditya Pokharna, Philipp Rössler et al.· Journal of Biomolecular NMR· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
