AIMC Topic: Protein Domains

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Exploring structural diversity across the protein universe with The Encyclopedia of Domains.

Science (New York, N.Y.) Nov 1, 2024
The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and functional contexts. Identifying domains can enabl...
Deep Learning Protein Domains Protein Folding Proteins Databases, Protein
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Deep learning for discriminating non-trivial conformational changes in molecular dynamics simulations of SARS-CoV-2 spike-ACE2.

Scientific reports Sep 30, 2024
Molecular dynamics (MD) simulations produce a substantial volume of high-dimensional data, and traditional methods for analyzing these data pose significant computational demands. Advances in MD simulation analysis combined with deep learning-based a...
Humans Binding Sites Protein Conformation Angiotensin-Converting Enzyme 2 Spike Glycoprotein, Coronavirus COVID-19 Deep Learning Mutation Protein Domains SARS-CoV-2 Protein Binding Molecular Dynamics Simulation
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A Machine Learning Approach to Identify C Type Lectin Domain (CTLD) Containing Proteins.

The protein journal Jul 28, 2024
Lectins are sugar interacting proteins which bind specific glycans reversibly and have ubiquitous presence in all forms of life. They have diverse biological functions such as cell signaling, molecular recognition, etc. C-type lectins (CTL) are a gro...
Protein Domains Humans Machine Learning Lectins, C-Type
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Versatile Framework for Drug-Target Interaction Prediction by Considering Domain-Specific Features.

Journal of chemical information and modeling Jul 8, 2024
Predicting drug-target interactions (DTIs) is one of the crucial tasks in drug discovery, but traditional wet-lab experiments are costly and time-consuming. Recently, deep learning has emerged as a promising tool for accelerating DTI prediction due t...
Deep Learning Proteins Drug Discovery Ligands Protein Domains Pharmaceutical Preparations
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Co-Mutations and Possible Variation Tendency of the Spike RBD and Membrane Protein in SARS-CoV-2 by Machine Learning.

International journal of molecular sciences Apr 25, 2024
Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, SARS-CoV-2 variants capable of breakthrough infections have attracted global attention. These variants have significant mutations in the receptor-binding domain (RBD) of the spike p...
Coronavirus M Proteins Protein Domains Amino Acid Sequence Mutation COVID-19 Humans Protein Binding SARS-CoV-2 Machine Learning Spike Glycoprotein, Coronavirus
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Analyzing domain features of small proteins using a machine-learning method.

Proteomics Jan 22, 2024
Small proteins (SPs) are a unique group of proteins that play crucial roles in many important biological processes. Exploring the biological function of SPs is necessary. In this study, the InterPro tool and the maximum correlation method were utiliz...
Protein Domains Proteins Databases, Protein Computational Biology Humans Machine Learning
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PPSNO: A Feature-Rich SNO Sites Predictor by Stacking Ensemble Strategy from Protein Sequence-Derived Information.

Interdisciplinary sciences, computational life sciences Jan 11, 2024
The protein S-nitrosylation (SNO) is a significant post-translational modification that affects the stability, activity, cellular localization, and function of proteins. Therefore, highly accurate prediction of SNO sites aids in grasping biological f...
Machine Learning Protein Processing, Post-Translational Proteins Protein Domains Amino Acid Sequence
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RefinePocket: An Attention-Enhanced and Mask-Guided Deep Learning Approach for Protein Binding Site Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Oct 9, 2023
Protein binding site prediction is an important prerequisite task of drug discovery and design. While binding sites are very small, irregular and varied in shape, making the prediction very challenging. Standard 3D U-Net has been adopted to predict b...
Binding Sites Drug Discovery Protein Binding Deep Learning Protein Domains Image Processing, Computer-Assisted
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E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning.

Journal of chemical information and modeling Oct 3, 2023
With the development of deep learning, almost all single-domain proteins can be predicted at experimental resolution. However, the structure prediction of multi-domain proteins remains a challenge. Achieving end-to-end protein domain assembly and fur...
Deep Learning Proteins Protein Domains
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AlphaFold-multimer predicts ATG8 protein binding motifs crucial for autophagy research.

PLoS biology Feb 8, 2023
In this issue of PLOS Biology, Ibrahim and colleagues demonstrate how AlphaFold-multimer, an artificial intelligence-based structure prediction tool, can be used to identify sequence motifs binding to the ATG8 family of proteins central to autophagy.
Protein Domains Protein Binding Artificial Intelligence Autophagy
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