AIMC Topic: Proteins

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AggNet: Advancing protein aggregation analysis through deep learning and protein language model.

Protein science : a publication of the Protein Society Feb 1, 2025
Protein aggregation is critical to various biological and pathological processes. Besides, it is also an important property in biotherapeutic development. However, experimental methods to profile protein aggregation are costly and labor-intensive, dr...
Proteins Models, Molecular Protein Aggregates Humans Deep Learning
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BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data.

Nucleic acids research Jan 6, 2025
BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, trai...
Protein Binding Proteins Databases, Protein Humans Binding Sites Internet Small Molecule Libraries Knowledge Bases
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UniProt: the Universal Protein Knowledgebase in 2025.

Nucleic acids research Jan 6, 2025
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication, we describe o...
Internet Knowledge Bases Molecular Sequence Annotation Proteins Machine Learning Databases, Protein Software Proteomics Proteome Animals Humans
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CGPDTA: An Explainable Transfer Learning-Based Predictor With Molecule Substructure Graph for Drug-Target Binding Affinity.

Journal of computational chemistry Jan 5, 2025
Identifying interactions between drugs and targets is crucial for drug discovery and development. Nevertheless, the determination of drug-target binding affinities (DTAs) through traditional experimental methods is a time-consuming process. Conventio...
Pharmaceutical Preparations Protein Binding Proteins Drug Discovery Molecular Structure Deep Learning
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Structure-Based Prediction of lncRNA-Protein Interactions by Deep Learning.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2025
The interactions between long noncoding RNA (lncRNA) and protein play crucial roles in various biological processes. Computational methods are essential for predicting lncRNA-protein interactions and deciphering their mechanisms. In this chapter, we ...
Proteins Humans RNA-Binding Proteins Deep Learning RNA, Long Noncoding Neural Networks, Computer Protein Binding Software Computational Biology
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SG-ML-PLAP: A structure-guided machine learning-based scoring function for protein-ligand binding affinity prediction.

Protein science : a publication of the Protein Society Jan 1, 2025
Computational methods to predict binding affinity of protein-ligand complex have been used extensively to design inhibitors for proteins selected as drug targets. In recent years machine learning (ML) is being increasingly used for design of drugs/in...
Molecular Docking Simulation Protein Binding Databases, Protein Ligands Proteins Machine Learning Software
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Beyond AlphaFold2: The Impact of AI for the Further Improvement of Protein Structure Prediction.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2025
Protein structure prediction is fundamental to molecular biology and has numerous applications in areas such as drug discovery and protein engineering. Machine learning techniques have greatly advanced protein 3D modeling in recent years, particularl...
Protein Folding Models, Molecular Protein Conformation Proteins Databases, Protein Neural Networks, Computer Software Machine Learning Computational Biology
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Machine Learning Techniques to Infer Protein Structure and Function from Sequences: A Comprehensive Review.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2025
The elucidation of protein structure and function plays a pivotal role in understanding biological processes and facilitating drug discovery. With the exponential growth of protein sequence data, machine learning techniques have emerged as powerful t...
Databases, Protein Structure-Activity Relationship Natural Language Processing Computational Biology Proteins Protein Conformation Humans Machine Learning Deep Learning Neural Networks, Computer
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DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning.

Bioinformatics (Oxford, England) Dec 26, 2024
MOTIVATION: The knowledge of protein stability upon residue variation is an important step for functional protein design and for understanding how protein variants can promote disease onset. Computational methods are important to complement experimen...
Databases, Protein Computational Biology Software Protein Stability Proteins Deep Learning
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Improving generalizability of drug-target binding prediction by pre-trained multi-view molecular representations.

Bioinformatics (Oxford, England) Dec 26, 2024
MOTIVATION: Most drugs start on their journey inside the body by binding the right target proteins. This is the reason that numerous efforts have been devoted to predicting the drug-target binding during drug development. However, the inherent divers...
Proteins Neural Networks, Computer Drug Discovery Binding Sites Humans Protein Binding Computational Biology
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