AIMC Topic: Proteins

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High-Throughput Analysis of Protein Adsorption to a Large Library of Polymers Using Liquid Extraction Surface Analysis-Tandem Mass Spectrometry (LESA-MS/MS).

Analytical chemistry Jun 10, 2025
Biomaterials play an important role in medicine from contact lenses to joint replacements. High-throughput screening coupled with machine learning has identified synthetic polymers that prevent bacterial biofilm formation, prevent fungal cell attachm...
High-Throughput Screening Assays Surface Properties Adsorption Proteins Tandem Mass Spectrometry Liquid-Liquid Extraction Polymers Machine Learning
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Designing diverse and high-performance proteins with a large language model in the loop.

PLoS computational biology Jun 5, 2025
We present a protein engineering approach to directed evolution with machine learning that integrates a new semi-supervised neural network fitness prediction model, Seq2Fitness, and an innovative optimization algorithm, biphasic annealing for diverse...
Algorithms Computational Biology Proteins Neural Networks, Computer Machine Learning Large Language Models Mutation Protein Engineering
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Multi-view based heterogeneous graph contrastive learning for drug-target interaction prediction.

Journal of biomedical informatics Jun 2, 2025
Drug-Target Interaction (DTI) prediction plays a pivotal role in accelerating drug discovery and development by identifying novel interactions between drugs and targets. Most previous studies on Drug-Protein Pair (DPP) networks have primarily focused...
Humans Neural Networks, Computer Drug Discovery Computational Biology Proteins Machine Learning Algorithms
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Measuring alignment of structural proteins in engineered tissue constructs using polarized Raman spectroscopy.

PloS one May 30, 2025
Measures of structural protein alignment within biological and engineered tissues are needed for improved understanding of their mechanical behavior and functionality. We advance our method of measuring protein alignment using polarized Raman spectro...
Tissue Engineering Proteins Myoblasts Spectrum Analysis, Raman Cell Line Animals Mice
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Prediction of drug-target interactions based on substructure subsequences and cross-public attention mechanism.

PloS one May 30, 2025
Drug-target interactions (DTIs) play a critical role in drug discovery and repurposing. Deep learning-based methods for predicting drug-target interactions are more efficient than wet-lab experiments. The extraction of original and substructural feat...
Pharmaceutical Preparations Data Mining Proteins Drug Repositioning Humans Drug Discovery Deep Learning Algorithms
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Explainability of Protein Deep Learning Models.

International journal of molecular sciences May 29, 2025
Protein embeddings are the new main source of information about proteins, producing state-of-the-art solutions to many problems, including protein interaction prediction, a fundamental issue in proteomics. Understanding the embeddings and what causes...
Proteins Hydrophobic and Hydrophilic Interactions Protein Interaction Mapping Computational Biology Proteomics Deep Learning
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Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange.

eLife May 27, 2025
Despite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformation...
Molecular Docking Simulation Protein Binding Proteins Protein Conformation Computational Biology Software Algorithms Protein Folding
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EMOCPD: Efficient Attention-Based Models for Computational Protein Design Using Amino Acid Microenvironment.

Journal of chemical information and modeling May 26, 2025
Computational protein design (CPD) refers to the use of computational methods to design proteins. Traditional methods relying on energy functions and heuristic algorithms for sequence design are inefficient and do not meet the demands of the big data...
Proteins Models, Molecular Amino Acids Computational Biology Protein Conformation Protein Engineering
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CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis.

Journal of chemical information and modeling May 22, 2025
Some functional proteins undergo conformational changes to expose hidden binding sites when a binding molecule approaches their surface. Such binding sites are called cryptic sites and are important targets for drug discovery. However, it is still di...
Protein Conformation Ligands Proteins Binding Sites Solvents Molecular Dynamics Simulation
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On the Difficulty to Rescore Hits from Ultralarge Docking Screens.

Journal of chemical information and modeling May 22, 2025
Docking-based virtual screening tools customized to mine ultralarge chemical spaces are consistently reported to yield both higher hit rates and more potent ligands than that achieved by conventional docking of smaller million-sized compound librarie...
Drug Evaluation, Preclinical Quantum Theory Protein Binding Proteins Ligands Machine Learning Molecular Docking Simulation
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