AIMC Topic: Protein Domains

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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...
Drug Discovery Deep Learning Pharmaceutical Preparations Ligands Proteins Protein Domains
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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...
Humans Amino Acid Sequence Coronavirus M Proteins Protein Binding Spike Glycoprotein, Coronavirus Mutation Machine Learning COVID-19 Protein Domains SARS-CoV-2
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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...
Databases, Protein Protein Domains Humans Machine Learning Computational Biology Proteins
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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 Amino Acid Sequence Proteins Protein Domains
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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...
Image Processing, Computer-Assisted Protein Binding Protein Domains Binding Sites Drug Discovery Deep Learning
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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...
Proteins Protein Domains Deep Learning
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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.
Artificial Intelligence Autophagy Protein Binding Protein Domains
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Neural Networks in the Design of Molecules with Affinity to Selected Protein Domains.

International journal of molecular sciences Jan 16, 2023
Drug design with machine learning support can speed up new drug discoveries. While current databases of known compounds are smaller in magnitude (approximately 108), the number of small drug-like molecules is estimated to be between 1023 and 1060. Th...
Bayes Theorem Neural Networks, Computer Molecular Docking Simulation Protein Domains Drug Design Artificial Intelligence
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Decoding CAR T cell phenotype using combinatorial signaling motif libraries and machine learning.

Science (New York, N.Y.) Dec 8, 2022
Chimeric antigen receptor (CAR) costimulatory domains derived from native immune receptors steer the phenotypic output of therapeutic T cells. We constructed a library of CARs containing ~2300 synthetic costimulatory domains, built from combinations ...
Receptors, Chimeric Antigen T-Lymphocytes, Cytotoxic Peptide Library Humans Signal Transduction Phenotype Machine Learning Protein Domains
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Learning Proteome Domain Folding Using LSTMs in an Empirical Kernel Space.

Journal of molecular biology Jun 15, 2022
The recognition of protein structural folds is the starting point for protein function inference and for many structural prediction tools. We previously introduced the idea of using empirical comparisons to create a data-augmented feature space calle...
Protein Domains Algorithms Neural Networks, Computer Protein Folding Proteome
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