AIMC Topic: Membrane Proteins

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Accurate classification of membrane protein types based on sequence and evolutionary information using deep learning.

BMC bioinformatics Dec 24, 2019
BACKGROUND: Membrane proteins play an important role in the life activities of organisms. Knowing membrane protein types provides clues for understanding the structure and function of proteins. Though various computational methods for predicting memb...
Deep Learning Computational Biology Membrane Proteins Sequence Analysis
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Propofol affects the growth and metastasis of pancreatic cancer via ADAM8.

Pharmacological reports : PR Dec 20, 2019
BACKGROUND: Anesthesia is a major component of surgery and recently considered an important regulator of cell phenotypes. Here we aimed to investigate propofol, an anesthesia drug, in suppressing pancreatic cancer (PDAC), focusing on A disintegrin an...
Mice, SCID Neoplasm Metastasis Cell Movement Cell Line, Tumor Apoptosis Membrane Proteins Humans MAP Kinase Signaling System Neoplasm Invasiveness Animals ADAM Proteins Cell Proliferation Antineoplastic Agents Propofol Pancreatic Neoplasms Matrix Metalloproteinase 9 Matrix Metalloproteinase 2 Xenograft Model Antitumor Assays
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A 21‑gene Support Vector Machine classifier and a 10‑gene risk score system constructed for patients with gastric cancer.

Molecular medicine reports Nov 21, 2019
Gastric cancer (GC) ranks fifth in terms of incidence and third in terms of tumor mortality worldwide. The present study was designed to construct a Support Vector Machine (SVM) classifier and risk score system for GC. The GSE62254 (training set) and...
Carrier Proteins Nerve Tissue Proteins Neoplasm Recurrence, Local Tumor Suppressor Proteins Membrane Proteins Support Vector Machine Databases, Genetic Kaplan-Meier Estimate Angiopoietin-like Proteins A Kinase Anchor Proteins Aged Angiopoietin-Like Protein 1 Cytokines Stomach Neoplasms Middle Aged Humans Prognosis Gene Expression Profiling Male Female Gene Regulatory Networks Risk Factors Gene Expression Regulation, Neoplastic
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Distance-based protein folding powered by deep learning.

Proceedings of the National Academy of Sciences of the United States of America Aug 9, 2019
Direct coupling analysis (DCA) for protein folding has made very good progress, but it is not effective for proteins that lack many sequence homologs, even coupled with time-consuming conformation sampling with fragments. We show that we can accurate...
Deep Learning Time Factors Membrane Proteins Models, Molecular Algorithms Protein Folding Sequence Alignment
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Efficient utilization on PSSM combining with recurrent neural network for membrane protein types prediction.

Computational biology and chemistry Aug 8, 2019
Position-Specific Scoring Matrix (PSSM) is an excellent feature extraction method that was proposed early in protein classifying prediction, but within the restriction of feature shape in PSSM, researchers make a lot attempts to process it so that PS...
Neural Networks, Computer Computational Biology Membrane Proteins Databases, Protein Position-Specific Scoring Matrices
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Prediction of ATP-binding sites in membrane proteins using a two-dimensional convolutional neural network.

Journal of molecular graphics & modelling Jul 15, 2019
Membrane proteins, the most important drug targets, account for around 30% of total proteins encoded by the genome of living organisms. An important role of these proteins is to bind adenosine triphosphate (ATP), facilitating crucial biological proce...
Position-Specific Scoring Matrices Binding Sites Amino Acid Motifs Web Browser ROC Curve Computational Biology Membrane Proteins Models, Theoretical Databases, Protein Amino Acid Sequence Adenosine Triphosphate Neural Networks, Computer Machine Learning Algorithms Reproducibility of Results
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Effect of potential probiotic Leuconostoc mesenteroides FB111 in prevention of cholesterol absorption by modulating NPC1L1/PPARα/SREBP-2 pathways in epithelial Caco-2 cells.

International microbiology : the official journal of the Spanish Society for Microbiology Dec 5, 2018
Mustard kimchi consumption reduces cholesterol levels in rats. To identify lactic acid bacteria (LAB) in kimchi which exert this effect, 20 LAB isolates were evaluated for cholesterol reduction in an in vitro screen. The FB111 strain showed the highe...
Real-Time Polymerase Chain Reaction Membrane Proteins Epithelial Cells Food Microbiology Probiotics Caco-2 Cells Cholesterol Humans Gene Expression Profiling Leuconostoc mesenteroides Sterol Regulatory Element Binding Protein 2 Membrane Transport Proteins PPAR alpha
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Higher serum levels of fibroblast growth factor 21 in old patients with cachexia.

Nutrition (Burbank, Los Angeles County, Calif.) Nov 22, 2018
OBJECTIVE: Fibroblast growth factor (FGF)21 is promptly induced by short fasting in animal models to regulate glucose and fat metabolism. Data on FGF21 in humans are inconsistent and FGF21 has not yet been investigated in old patients with cachexia, ...
Gelatinases Serine Endopeptidases Fibroblast Growth Factors Endopeptidases Cachexia Humans Prospective Studies Female Male Aged Pilot Projects Aged, 80 and over Weight Loss Cross-Sectional Studies Membrane Proteins
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Predicting membrane protein types by incorporating a novel feature set into Chou's general PseAAC.

Journal of theoretical biology Jul 27, 2018
Membrane proteins are vital type of proteins that serve as channels, receptors and energy transducers in a cell. They perform various important functions, which are mainly associated with their types. They are also attractive targets of drug discover...
Support Vector Machine Databases, Protein Sequence Analysis, Protein Software Membrane Proteins
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iMem-2LSAAC: A two-level model for discrimination of membrane proteins and their types by extending the notion of SAAC into chou's pseudo amino acid composition.

Journal of theoretical biology Jan 11, 2018
Membrane proteins execute significant roles in cellular processes of living organisms, ranging from cell signaling to cell adhesion. As a major part of a cell, the identification of membrane proteins and their functional types become a challenging jo...
Computational Biology Membrane Proteins Neural Networks, Computer Support Vector Machine Algorithms Amino Acid Sequence Databases, Protein Reproducibility of Results Sequence Analysis, Protein
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