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In order to successfully predict a protein's function throughout its trajectory, in addition to uncovering changes in its conformational state, it is necessary to employ techniques that maintain its 3D information while performing at scale. We propose a protein representation that encodes secondary and tertiary structure into fix-sized, color images, and a neural network architecture (called GEM-net) that leverages our encoded representation. We show the applicability of our method in two ways: (1) performing protein function prediction, hitting accuracies between 78 and 83%, and (2) visualizing and detecting conformational changes in protein trajectories during molecular dynamics simulations.
This article was published in the following journal.
Name: IEEE/ACM transactions on computational biology and bioinformatics
As the first step of machine-learning based protein structure and function prediction, the amino acid encoding play a fundamental role in the final success of those methods. Different with the protein...
Classification of protein sequences is one big task in bioinformatics and has many applications. Different machine learning methods exist and are applied on these problems, such as support vector mach...
To reveal the working pattern of programmed cell death, knowledge of the subcellular location of apoptosis proteins is essential. Besides the costly and time-consuming method of experimental determina...
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In image classification, it is often expensive and time-consuming to acquire sufficient labels. To solve this problem, domain adaptation often provides an attractive option given a large amount of lab...
The evaluation of protein quality has been identified as the top priority question by the Food and Agricultural Organization (FAO) of the United Nations. However, the current available met...
The aim of this study is to compare different sugary drink labels to see which most influence knowledge, beliefs, purchase intentions and choices. Parents of children ages 6-11 will shop i...
The study intends to provide important data on whether the noval method using quantitative flow ratio could assess microcirculation.
A classification method describing the larynx appearance during laryngoscopy accepted by all anesthetists has not been defined yet. In one study, it was shown that anesthetists mis classed...
Malnutrition affects 50% to 70% of hospitalized elderly people, and is all the more worrying in the elderly because of its clinical impact. A measurement of food consumption is essential t...
A quantitative prediction of the biological, ecotoxicological or pharmaceutical activity of a molecule. It is based upon structure and activity information gathered from a series of similar compounds.
Locations, on the GENOME, of GENES or other genetic elements that encode or control the expression of a quantitative trait (QUANTITATIVE TRAIT, HERITABLE).
The World Health Organization's classification categories of health and health-related domains. The International Classification of Functioning, Disability and Health (ICF) consists of two lists: a list of body functions and structure, and a list of domains of activity and participation. The ICF also includes a list of environmental factors.
Technique of graphic representation of the movements of the body imparted by the ballistic forces (recoil and impact) associated with cardiac contraction and ejection of blood and with the deceleration of blood flow through the large blood vessels. These movements, quantitatively very minute, are translated by a pickup device (transducer) into an electrical potential which is suitably amplified and recorded on a conventional electrocardiograph or other recording machine.
A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...