AIMC Topic: Proteins

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ACDMBI: A deep learning model based on community division and multi-source biological information fusion predicts essential proteins.

Computational biology and chemistry
Accurately identifying essential proteins is vital for drug research and disease diagnosis. Traditional centrality methods and machine learning approaches often face challenges in accurately discerning essential proteins, primarily relying on informa...

EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks.

International journal of molecular sciences
Reliable and accurate methods of estimating the accuracy of predicted protein models are vital to understanding their respective utility. Discerning how the quaternary structure conforms can significantly improve our collective understanding of cell ...

PTransIPs: Identification of Phosphorylation Sites Enhanced by Protein PLM Embeddings.

IEEE journal of biomedical and health informatics
Phosphorylation is pivotal in numerous fundamental cellular processes and plays a significant role in the onset and progression of various diseases. The accurate identification of these phosphorylation sites is crucial for unraveling the molecular me...

SOFB is a comprehensive ensemble deep learning approach for elucidating and characterizing protein-nucleic-acid-binding residues.

Communications biology
Proteins and nucleic-acids are essential components of living organisms that interact in critical cellular processes. Accurate prediction of nucleic acid-binding residues in proteins can contribute to a better understanding of protein function. Howev...

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Proteomics
RNA-dependent liquid-liquid phase separation (LLPS) proteins play critical roles in cellular processes such as stress granule formation, DNA repair, RNA metabolism, germ cell development, and protein translation regulation. The abnormal behavior of t...

Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences.

Proteins
We apply methods of Artificial Intelligence and Machine Learning to protein dynamic bioinformatics. We rewrite the sequences of a large protein data set, containing both folded and intrinsically disordered molecules, using a representation developed ...

DSSGNN-PPI: A Protein-Protein Interactions prediction model based on Double Structure and Sequence graph neural networks.

Computers in biology and medicine
The process of experimentally confirming complex interaction networks among proteins is time-consuming and laborious. This study aims to address Protein-Protein Interactions (PPIs) prediction based on graph neural networks (GNN). A novel multilevel p...

Protein-Protein Interfaces: A Graph Neural Network Approach.

International journal of molecular sciences
Protein-protein interactions (PPIs) are fundamental processes governing cellular functions, crucial for understanding biological systems at the molecular level. Compared to experimental methods for PPI prediction and site identification, computationa...

PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction.

Journal of bioinformatics and computational biology
Biomolecular interaction recognition between ligands and proteins is an essential task, which largely enhances the safety and efficacy in drug discovery and development stage. Studying the interaction between proteins and ligands can improve the unde...

NPEX: Never give up protein exploration with deep reinforcement learning.

Journal of molecular graphics & modelling
Elucidating unknown structures of proteins, such as metastable states, is critical in designing therapeutic agents. Protein structure exploration has been performed using advanced computational methods, especially molecular dynamics and Markov chain ...