AIMC Topic: Proteins

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Enhancing Drug-Target Interaction Prediction through Transfer Learning from Activity Cliff Prediction Tasks.

Journal of chemical information and modeling Jul 14, 2025
Recently, machine learning (ML) has gained popularity in the early stages of drug discovery. This trend is unsurprising given the increasing volume of relevant experimental data and the continuous improvement of ML algorithms. However, conventional m...
Pharmaceutical Preparations Drug Discovery Machine Learning Proteins
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CAML: Commutative Algebra Machine Learning─A Case Study on Protein-Ligand Binding Affinity Prediction.

Journal of chemical information and modeling Jul 14, 2025
Recently, Suwayyid and Wei introduced commutative algebra as an emerging paradigm for machine learning and data science. In this work, we propose commutative algebra machine learning (CAML) for the prediction of protein-ligand binding affinities. Spe...
Algorithms Machine Learning Proteins Protein Binding Ligands
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Computer-Aided Drug Discovery for Undruggable Targets.

Chemical reviews Jul 9, 2025
Undruggable targets are those of therapeutical significance but challenging for conventional drug design approaches. Such targets often exhibit unique features, including highly dynamic structures, a lack of well-defined ligand-binding pockets, the p...
Intrinsically Disordered Proteins Allosteric Regulation Drug Discovery Proteins Ligands Computer-Aided Design Drug Design Humans Artificial Intelligence
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PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis.

Nucleic acids research Jul 7, 2025
Knowledge of protein-ligand binding sites (LBSs) is crucial for advancing our understanding of biology and developing practical applications in fields such as medicine or biotechnology. PrankWeb is a web server that allows users to predict LBSs from ...
Protein Binding Proteins Internet Machine Learning Molecular Docking Simulation Binding Sites Software User-Computer Interface Ligands Protein Conformation
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DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation.

Nucleic acids research Jul 7, 2025
Atomic structure modeling is a crucial step in determining the structures of protein complexes using cryo-electron microscopy (cryo-EM). This work introduces DEMO-EMol, an improved server that integrates deep learning-based map segmentation and chain...
Proteins Software Protein Conformation Cryoelectron Microscopy Models, Molecular Nucleic Acid Conformation Deep Learning Nucleic Acids
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InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep.

Nucleic acids research Jul 7, 2025
Predicting functional binding sites in proteins is crucial for understanding protein-protein interactions (PPIs) and identifying drug targets. While various computational approaches exist, many fail to assess PPI ligandability, which often involves c...
Protein Interaction Mapping Protein Conformation Binding Sites Proteins Databases, Protein Internet Ligands Models, Molecular Deep Learning Software Protein Binding Computational Biology
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HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.

Nucleic acids research Jul 7, 2025
Protein-protein interactions (PPIs) are fundamental to cellular functions, yet predicting and analyzing their 3D structures remains a critical and computationally demanding challenge. To address this, the HawkDock web server was developed as an integ...
Software Molecular Docking Simulation Computational Biology Proteins Mutation Deep Learning Protein Binding Protein Interaction Mapping Multiprotein Complexes Internet Protein Conformation
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StructMAn 2.0 Web: a web server for structural annotation of protein sequences and mutations.

Nucleic acids research Jul 7, 2025
StructMAn is a method for protein structural annotation. It describes each position of a protein sequence or specific variants in it in terms of their importance for the three-dimensional (3D) structure of the protein and its interactions with other ...
Molecular Sequence Annotation Sequence Analysis, Protein User-Computer Interface Amino Acid Sequence Software Proteins Protein Conformation Mutation Models, Molecular Internet
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FoldScript: a web server for the efficient analysis of AI-generated 3D protein models.

Nucleic acids research Jul 7, 2025
Artificial intelligence (AI)-based 3D protein modelling software have revolutionized structural biology, often predicting protein structures with unprecedented confidence. However, to get the most out of AI, it is advisable to consider the informatio...
Artificial Intelligence Models, Molecular Internet Protein Conformation Software Proteins
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GOBeacon: An ensemble model for protein function prediction enhanced by contrastive learning.

Protein science : a publication of the Protein Society Jul 1, 2025
Accurate prediction of protein function is fundamental to understanding biological processes, with computational methods becoming increasingly essential as experimental methods struggle to keep pace with the rate of newly discovered proteins. Despite...
Databases, Protein Machine Learning Software Computational Biology Proteins
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