AIMC Topic: Hydrophobic and Hydrophilic Interactions
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Discrimination power of knowledge-based potential dictated by the dominant energies in native protein structures.
Amino acids
May 16, 2019
Extracting a well-designed energy function is important for protein structure evaluation. Knowledge-based potential functions are one type of the energy functions which can be obtained from known protein structures. The pairwise potential between ato...
In silico minimalist approach to study 2D HP protein folding into an inhomogeneous space mimicking osmolyte effect: First trial in the search of foldameric backbones.
Bio Systems
Apr 25, 2019
We have employed our bioinformatics workbench, named Evolution, a Multi-Agent System based architecture with lattice-bead-models, evolutionary-algorithms, and correlated-networks as inhomogeneous spaces, with different correlation lengths, mimicking ...
Prediction of Hemolytic Toxicity for Saponins by Machine-Learning Methods.
Chemical research in toxicology
Apr 9, 2019
Saponins are a type of compounds bearing a hydrophobic steroid/triterpenoid moiety and hydrophilic carbohydrate branches. The majority of the saponins demonstrate a broad range of prominent pharmacological activities. Nevertheless, many saponins also...
Discovery of small molecule binders of human FSHR(TMD) with novel structural scaffolds by integrating structural bioinformatics and machine learning algorithms.
Journal of molecular graphics & modelling
Mar 5, 2019
BACKGROUND: The activation of follicle stimulating hormone receptor (FSHR) by FSH and the consequent downstream signaling activities are crucial for reproductive health. The role of FSHR in tumor progression as well as osteoporosis advancement has al...
Shape-Based Generative Modeling for de Novo Drug Design.
Journal of chemical information and modeling
Feb 28, 2019
In this work, we propose a machine learning approach to generate novel molecules starting from a seed compound, its three-dimensional (3D) shape, and its pharmacophoric features. The pipeline draws inspiration from generative models used in image ana...
Hypoxia-responsive micelles self-assembled from amphiphilic block copolymers for the controlled release of anticancer drugs.
Journal of materials chemistry. B
Dec 12, 2018
Amphiphilic block copolymers poly(ethylene glycol)-block-poly(methacrylic acid-co-2-nitroimidazole methacrylate) (PEG-b-P(MAA-co-NIMA)) were synthesized by the combination of atom transfer radical polymerization (ATRP), hydrolysis and EDC reactions. ...
Delimiting the knowledge space and the design space of nanostructured lipid carriers through Artificial Intelligence tools.
International journal of pharmaceutics
Oct 26, 2018
Nanostructured lipid carriers (NLC) are biocompatible and biodegradable nanoscale systems with extensive application for controlled drug release. However, the development of optimal nanosystems along with a reproducible manufacturing process is still...
The antibacterial activity of rhamnolipid biosurfactant is pH dependent.
Food research international (Ottawa, Ont.)
Sep 6, 2018
Rhamnolipid (RL) biosurfactants have been studied as agents to control the growth of food pathogens however, to be successful applied as antimicrobial agent in food, is important to determine the effect of environmental conditions on RL activity. Onc...
Protein Solvent-Accessibility Prediction by a Stacked Deep Bidirectional Recurrent Neural Network.
Biomolecules
May 25, 2018
Residue solvent accessibility is closely related to the spatial arrangement and packing of residues. Predicting the solvent accessibility of a protein is an important step to understand its structure and function. In this work, we present a deep lear...
Robotic Patterning a Superhydrophobic Surface for Collective Cell Migration Screening.
Tissue engineering. Part C, Methods
Mar 27, 2018
Collective cell migration, in which cells migrate as a group, is fundamental in many biological and pathological processes. There is increasing interest in studying the collective cell migration in high throughput. Cell scratching, insertion blocker,...
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