Here you can find the data from the study "Quadrupling the protein family space with global metagenomics". For Protein Families: iso_clusters25_names.tsv.bz2 Description: TSV file of isolate clusters with more than 25 members. Columns: (1)Cluster name (2)Representative isolate protein header (3) Isolate protein member...
Eleni Aplakidou, Fotis A. Baltoumas, Georgios A. Pavlopoulos· Zenodo (CERN European Organi...· 0 citations
Repeat proteins fold through pathways that are strongly shaped by local energetics, making them highly sensitive to mutations. The ankyrin repeat (AR) domain of IκBα is a cooperative folding unit in which the first four repeats (AR1–AR4) are stable, while the last two are destabilized. Despite this simple modular archi...
Murilo N. Sanches, María Inés Freiberger, Peter G. Wolynes et al.· Zenodo (CERN European Organi...· 0 citations
Molecular dynamics (MD) simulations are a fundamental tool in materials science, biology, and pharmaceutical research, offering insights into molecular behavior and dynamics. However, traditional MD simulations often suffer from limitations in accuracy and efficiency, particularly when dealing with complex, dynamic env...
Jincheng Zhang· Zenodo (CERN European Organi...· 0 citations
Optical tweezers using metal nanostructures have leveraged extreme subwavelength focusing to circumvent the diffraction limit, enabling the isolation and label-free sensing of single nanoparticles. Over the past two decades, nanoaperture optical tweezers (NOTs) have matured into a useful tool for biophysical analysis,...
Reuven Gordon· Journal of Physics: Photonic...· 0 citations
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Lignocellulosic biomass is one of the most abundantly available renewable energy sources, but it is entirely underutilized. Composed of a matrix of cellulose and hemicellulose polysaccharides, biochemical deconstruction of this substrate can yield fermentable sugars for biofuel production. Within a typical biorefinery,...
Antonio De Chellis· Rutgers University Community...· 0 citations
The results suggest that the increased heat tolerance of T. californicus may be driven by a combination of these emergent proteins, several proteins induced by hypersalinity in both single- and multi-stressor conditions that may contribute to cross-tolerance, and four proteins with additive abundance patterns.
Caroline E. Terry, Maxime Leprêtre, D. Kültz et al.· Physiological Genomics· 0 citations
Derived data, run outputs and figure source data supporting the article "Joint optimisation of amino acid and coding sequence for de novo designed proteins". Includes the inverse-folding marginals for all 862 backbones and the full 230,992-row double-mutant additivity table.
Anees Ahmed Mahaboob Ali, Radhakrishnan Delhibabu, Everette Jacob Remington Nelson· Zenodo (CERN European Organi...· 0 citations
Overview A prospectively frozen benchmark suite for leakage-safe multi-omic integration. It tests predictive performance, modality utility, model-capacity effects, missingness handling, null behavior, exploratory external transport, failure handling, and compute cost without making claims of clinical utility or causal...
TUNA BİRGÜN· Zenodo (CERN European Organi...· 0 citations
This research investigates the application of non-linear constraint optimization to biological systems, specifically focusing on optimization of gene expression and protein folding. Traditional optimization methods often struggle with the inherent complexity and dynamic nature of biological systems, necessitating novel...
Jincheng Zhang· Zenodo (CERN European Organi...· 0 citations
Design principles that produces a robust and efficient heat shock response are revealed, including regimes of synergy as well as trade-offs between speed and efficiency, with wild-type parameters lying near the optimal region.
Uremic conditions are common in end-stage kidney disease (ESKD) patients. Accelerated vascular diseases in uremic patients lead to heart failure, stroke, and hypertension. To investigate the effects of uremia on porcine arterial smooth muscle cells (aSMCs), bulk RNA sequencing was used to identify uremia-induced altera...
Unimunkh Uriyanghai, Huanjuan Su, John S. Poulton et al.· UNC Libraries· 0 citations
Temporal Wave Function Collapse Dynamics explores the theoretical underpinnings of the collapse of temporal wave functions – fundamental units of information within complex systems such as neural networks and protein folding – as a dynamic process. This paper posits that collapse isn't a discrete event but rather a con...
Jincheng Zhang· Zenodo (CERN European Organi...· 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.
