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Membrane Proteins

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Anti-inflammatory and antibacterial activities of P. petiolosa (Christ) Ching ethyl acetate extract against S. aureus in mice.

Pakistan journal of pharmaceutical sciences
P. petiolosa as a typical Chinese herbal medicine has been generally utilized as Chinese native medicine formulation for treatment of chronic bronchitis, bronchial asthma and pneumoconiosis. The objective of this study was to evaluate the anti-inflam...

Ensemble learning models that predict surface protein abundance from single-cell multimodal omics data.

Methods (San Diego, Calif.)
Single-cell protein abundance is a fundamental type of information to characterize cell states. Due to high cost and technical barriers, however, direct quantification of proteins is difficult. Single-cell RNA sequencing (scRNA-seq) data, serving as ...

Analyzing protein dynamics from fluorescence intensity traces using unsupervised deep learning network.

Communications biology
We propose an unsupervised deep learning network to analyze the dynamics of membrane proteins from the fluorescence intensity traces. This system was trained in an unsupervised manner with the raw experimental time traces and synthesized ones, so nei...

Regression plane concept for analysing continuous cellular processes with machine learning.

Nature communications
Biological processes are inherently continuous, and the chance of phenotypic discovery is significantly restricted by discretising them. Using multi-parametric active regression we introduce the Regression Plane (RP), a user-friendly discovery tool e...

In-Pero: Exploiting Deep Learning Embeddings of Protein Sequences to Predict the Localisation of Peroxisomal Proteins.

International journal of molecular sciences
Peroxisomes are ubiquitous membrane-bound organelles, and aberrant localisation of peroxisomal proteins contributes to the pathogenesis of several disorders. Many computational methods focus on assigning protein sequences to subcellular compartments,...

Highly accurate protein structure prediction for the human proteome.

Nature
Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. After decades of effort, 17% of the total residues i...

Accurate prediction of protein structures and interactions using a three-track neural network.

Science (New York, N.Y.)
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track ...

Loop-mediated isothermal amplification (LAMP) and machine learning application for early pregnancy detection using bovine vaginal mucosal membrane.

Biochemical and biophysical research communications
An early and accurate pregnancy diagnosis method is required to improve the reproductive performance of cows. Here we developed an easy pregnancy detection method using vaginal mucosal membrane (VMM) with application of Reverse Transcription-Loop-med...

Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method.

Bioinformatics (Oxford, England)
MOTIVATION: The solvent accessible surface is an essential structural property measure related to the protein structure and protein function. Relative solvent accessible area (RSA) is a standard measure to describe the degree of residue exposure in t...

PolarProtPred: predicting apical and basolateral localization of transmembrane proteins using putative short linear motifs and deep learning.

Bioinformatics (Oxford, England)
MOTIVATION: Cell polarity refers to the asymmetric organization of cellular components in various cells. Epithelial cells are the best-known examples of polarized cells, featuring apical and basolateral membrane domains. Mounting evidence suggests th...