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Metabolic Fluxes Using Deep Learning Based on Enzyme Variations: .
Int J Mol Sci
December 2024
BIGR, UMR_S1134 Inserm, University of Paris City, 75006 Paris, France.
Metabolic pathway modeling, essential for understanding organism metabolism, is pivotal in predicting genetic mutation effects, drug design, and biofuel development. Enhancing these modeling techniques is crucial for achieving greater prediction accuracy and reliability. However, the limited experimental data or the complexity of the pathway makes it challenging for researchers to predict phenotypes.
View Article and Find Full Text PDFMachine learning-based modulation of Ca-binding affinity in EF-hand proteins and comparative structural insights into site-specific cooperative binding.
Int J Biol Macromol
September 2023
School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India. Electronic address:
Ca-binding proteins are present in almost all living organisms and different types display different levels of binding affinities for the cation. Here, we report two new scoring schemes enabling the user to estimate and manipulate the calcium binding affinities in EF hand containing proteins. To validate this, we designed a unique EF-hand loop capable of binding calcium with high affinity by altering five residues.
View Article and Find Full Text PDFNon-linearity of Metabolic Pathways Critically Influences the Choice of Machine Learning Model.
Front Artif Intell
June 2022
University of Paris, BIGR-Biologie Intégrée du Globule Rouge, Inserm, UMR_S1134, Paris, France.
The use of machine learning (ML) in life sciences has gained wide interest over the past years, as it speeds up the development of high performing models. Important modeling tools in biology have proven their worth for pathway design, such as mechanistic models and metabolic networks, as they allow better understanding of mechanisms involved in the functioning of organisms. However, little has been done on the use of ML to model metabolic pathways, and the degree of non-linearity associated with them is not clear.
View Article and Find Full Text PDFFulminant necrotizing amoebic colitis presenting as acute appendicitis: a case report and comprehensive literature review.
J Infect Dev Ctries
April 2022
Department of Anatomical Pathology, Faculty of Medicine, Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia.
Intestinal amoebiasis is a parasitic infection caused by Entamoeba histolytica. It is commonly found in developing countries with poor hygiene. A rare, life-threatening complication of amoebiasis is fulminant necrotizing amoebic colitis (FulNAC).
View Article and Find Full Text PDFEntamoeba histolytica Develops Resistance to Complement Deposition and Lysis after Acquisition of Human Complement-Regulatory Proteins through Trogocytosis.
mBio
April 2022
Department of Microbiology and Molecular Genetics, University of California, Davisgrid.27860.3b, Davis, California, USA.
Entamoeba histolytica is the cause of amoebiasis. The trophozoite (amoeba) form of this parasite is capable of invading the intestine and can disseminate through the bloodstream to other organs. The mechanisms that allow amoebae to evade complement deposition during dissemination have not been well characterized.
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