AIMC Topic: Proteins

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Evaluation of Machine Learning/Molecular Mechanics End-State Corrections with Mechanical Embedding to Calculate Relative Protein-Ligand Binding Free Energies.

Journal of chemical theory and computation Jan 3, 2025
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are several ti...
Machine Learning Molecular Dynamics Simulation Quantum Theory Ligands Protein Binding Proteins Thermodynamics
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DPFunc: accurately predicting protein function via deep learning with domain-guided structure information.

Nature communications Jan 2, 2025
Computational methods for predicting protein function are of great significance in understanding biological mechanisms and treating complex diseases. However, existing computational approaches of protein function prediction lack interpretability, mak...
Protein Domains Protein Conformation Computational Biology Proteins Structure-Activity Relationship Models, Molecular Algorithms Databases, Protein Humans Deep Learning
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PharmRL: pharmacophore elucidation with deep geometric reinforcement learning.

BMC biology Dec 31, 2024
BACKGROUND: Molecular interactions between proteins and their ligands are important for drug design. A pharmacophore consists of favorable molecular interactions in a protein binding site and can be utilized for virtual screening. Pharmacophores are ...
Binding Sites Pharmacophore Proteins Ligands Drug Design Deep Learning Humans Algorithms
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Site-specific prediction of O-GlcNAc modification in proteins using evolutionary scale model.

PloS one Dec 31, 2024
Protein glycosylation, a vital post-translational modification, is pivotal in various biological processes and disease pathogenesis. Computational approaches, including protein language models and machine learning algorithms, have emerged as valuable...
Proteins Databases, Protein Glycosylation Protein Processing, Post-Translational Algorithms Acetylglucosamine Humans Glycoproteins Computational Biology Evolution, Molecular Machine Learning
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DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction.

Scientific reports Dec 30, 2024
Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robust de novo protein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Tradi...
Bacterial Proteins Microbiota Software Bacteria Computational Biology Deep Learning Gene Ontology Proteins
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CPI-GGS: A deep learning model for predicting compound-protein interaction based on graphs and sequences.

Computational biology and chemistry Dec 29, 2024
BACKGROUND: Compound-protein interaction (CPI) is essential to drug discovery and design, where traditional methods are often costly and have low success rates. Recently, the integration of machine learning and deep learning in CPI research has shown...
Proteins Drug Discovery Deep Learning Humans
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Porter 6: Protein Secondary Structure Prediction by Leveraging Pre-Trained Language Models (PLMs).

International journal of molecular sciences Dec 27, 2024
Accurately predicting protein secondary structure (PSSP) is crucial for understanding protein function, which is foundational to advancements in drug development, disease treatment, and biotechnology. Researchers gain critical insights into protein f...
Software Natural Language Processing Algorithms Protein Structure, Secondary Computational Biology Deep Learning Proteins
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Evaluations of the Perturbation Resistance of the Deep-Learning-Based Ligand Conformation Optimization Algorithm.

Journal of chemical information and modeling Dec 26, 2024
In recent years, the deep learning (DL) technique has rapidly developed and shown great success in scoring the protein-ligand binding affinities. The protein-ligand conformation optimization based on DL-derived scoring functions holds broad applicati...
Ligands Protein Conformation Protein Binding Proteins Molecular Docking Simulation Deep Learning Algorithms
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Topology-based protein classification: A deep learning approach.

Biochemical and biophysical research communications Dec 24, 2024
Utilizing Artificial Intelligence (AI) in computational biology techniques could offer significant advantages in alleviating the growing workloads faced by structural biologists, especially with the emergence of big data. In this study, we employed D...
Deep Learning Computational Biology Databases, Protein Protein Conformation Neural Networks, Computer Proteins
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A 4D tensor-enhanced multi-dimensional convolutional neural network for accurate prediction of protein-ligand binding affinity.

Molecular diversity Dec 23, 2024
Protein-ligand interactions are the molecular basis of many important cellular activities, such as gene regulation, cell metabolism, and signal transduction. Protein-ligand binding affinity is a crucial metric of the strength of the interaction betwe...
Neural Networks, Computer Deep Learning Convolutional Neural Networks Models, Molecular Ligands Protein Binding Binding Sites Proteins
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