AIMC Topic: Proteins

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CollaPPI: A Collaborative Learning Framework for Predicting Protein-Protein Interactions.

IEEE journal of biomedical and health informatics May 6, 2024
Exploring protein-protein interaction (PPI) is of paramount importance for elucidating the intrinsic mechanism of various biological processes. Nevertheless, experimental determination of PPI can be both time-consuming and expensive, motivating the e...
Humans Algorithms Proteins Databases, Protein Protein Interaction Mapping Deep Learning Computational Biology
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MR2CPPIS: Accurate prediction of protein-protein interaction sites based on multi-scale Res2Net with coordinate attention mechanism.

Computers in biology and medicine May 3, 2024
Proteins play a vital role in various biological processes and achieve their functions through protein-protein interactions (PPIs). Thus, accurate identification of PPI sites is essential. Traditional biological methods for identifying PPIs are costl...
Protein Interaction Mapping Proteins Databases, Protein Humans Deep Learning Computational Biology
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Machine-Learning-Aided Understanding of Protein Adsorption on Zwitterionic Polymer Brushes.

ACS applied materials & interfaces May 3, 2024
Constructing antifouling surfaces is a crucial technique for optimizing the performance of devices such as water treatment membranes and medical devices in practical environments. These surfaces are achieved by modification with hydrophilic polymers....
Surface Properties Proteins Biofouling Polymers Hydrophobic and Hydrophilic Interactions Molecular Weight Animals Adsorption Machine Learning
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A systematic analysis of regression models for protein engineering.

PLoS computational biology May 3, 2024
To optimize proteins for particular traits holds great promise for industrial and pharmaceutical purposes. Machine Learning is increasingly applied in this field to predict properties of proteins, thereby guiding the experimental optimization process...
Machine Learning Regression Analysis Proteins Algorithms Computational Biology Protein Engineering
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Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning.

The journal of physical chemistry. A Apr 29, 2024
Solvatochromism occurs in both homogeneous solvents and more complex biological environments, such as proteins. While in both cases the solvatochromic effects report on the surroundings of the chromophore, their interpretation in proteins becomes mor...
Solvents Molecular Dynamics Simulation Machine Learning Carotenoids Quantum Theory Proteins
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Deep learning for low-data drug discovery: Hurdles and opportunities.

Current opinion in structural biology Apr 25, 2024
Deep learning is becoming increasingly relevant in drug discovery, from de novo design to protein structure prediction and synthesis planning. However, it is often challenged by the small data regimes typical of certain drug discovery tasks. In such ...
Deep Learning Proteins Humans Drug Discovery
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Generative artificial intelligence for de novo protein design.

Current opinion in structural biology Apr 24, 2024
Engineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called 'de novo' design problem have recently been brought forwar...
Protein Engineering Models, Molecular Protein Conformation Artificial Intelligence Proteins
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Model fusion for predicting unconventional proteins secreted by exosomes using deep learning.

Proteomics Apr 21, 2024
Unconventional secretory proteins (USPs) are vital for cell-to-cell communication and are necessary for proper physiological processes. Unlike classical proteins that follow the conventional secretory pathway via the Golgi apparatus, these proteins a...
Humans Neural Networks, Computer Algorithms Amino Acid Sequence Proteins Exosomes Deep Learning Computational Biology
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Differentiating stable and unstable protein using convolution neural network and molecular dynamics simulations.

Computational biology and chemistry Apr 20, 2024
Protein stability is a critical aspect of molecular biology and biochemistry, hinges on an intricate balance of thermodynamic and structural factors. Determining protein stability is crucial for understanding and manipulating biological machineries, ...
Protein Stability Thermodynamics Proteins Molecular Dynamics Simulation Neural Networks, Computer Machine Learning
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Molecular Docking Improved with Human Spatial Perception Using Virtual Reality.

IEEE transactions on visualization and computer graphics Apr 19, 2024
Adaptive steered molecular dynamics (ASMD) is a computational biophysics method in which an external force is applied to a selected set of atoms or a specific reaction coordinate to induce a particular molecular motion. Virtual reality (VR) based met...
Computer Graphics Ligands Perception Virtual Reality Proteins Humans Artificial Intelligence Molecular Docking Simulation
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