AIMC Topic: Models, Molecular

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Uncovering substrate specificity determinants of class IIb aminoacyl-tRNA synthetases with machine learning.

Journal of molecular graphics & modelling Jul 14, 2024
Specific amino acid (AA) binding by aminoacyl-tRNA synthetases (aaRSs) is necessary for correct translation of the genetic code. Sequence and structure analyses have revealed the main specificity determinants and allowed a partitioning of aaRSs into ...
Substrate Specificity Amino Acyl-tRNA Synthetases Models, Molecular Amino Acid Sequence Machine Learning
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Scaffold-Hopped Compound Identification by Ligand-Based Approaches with a Prospective Affinity Test.

Journal of chemical information and modeling Jul 1, 2024
Scaffold-hopped (SH) compounds are bioactive compounds structurally different from known active compounds. Identifying SH compounds in the ligand-based approaches has been a central issue in medicinal chemistry, and various molecular representations ...
Humans Models, Molecular Algorithms Ligands Support Vector Machine Protein Kinase Inhibitors
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Deep-learning map segmentation for protein X-ray crystallographic structure determination.

Acta crystallographica. Section D, Structural biology Jun 27, 2024
When solving a structure of a protein from single-wavelength anomalous diffraction X-ray data, the initial phases obtained by phasing from an anomalously scattering substructure usually need to be improved by an iterated electron-density modification...
Models, Molecular Crystallography, X-Ray Proteins Neural Networks, Computer Protein Conformation Databases, Protein Deep Learning
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Classifying and Predicting the Thermal Expansion Properties of Metal-Organic Frameworks: A Data-Driven Approach.

Journal of chemical information and modeling Jun 26, 2024
Metal-organic frameworks (MOFs) are versatile materials for a wide variety of potential applications. Tunable thermal expansion properties promote the application of MOFs in thermally sensitive composite materials; however, they are currently availab...
Temperature Models, Molecular Metal-Organic Frameworks Machine Learning
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TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides.

Journal of chemical information and modeling Jun 26, 2024
The intricate interaction between major histocompatibility complexes (MHCs) and antigen peptides with diverse amino acid sequences plays a pivotal role in immune responses and T cell activity. In recent years, deep learning (DL)-based models have eme...
Models, Molecular Amino Acid Sequence Protein Conformation Deep Learning HLA-A2 Antigen Humans Protein Binding Peptides
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Accurate prediction of CDR-H3 loop structures of antibodies with deep learning.

eLife Jun 26, 2024
Accurate prediction of the structurally diverse complementarity determining region heavy chain 3 (CDR-H3) loop structure remains a primary and long-standing challenge for antibody modeling. Here, we present the H3-OPT toolkit for predicting the 3D st...
Protein Conformation Single-Domain Antibodies Humans Antibodies, Monoclonal Complementarity Determining Regions Models, Molecular Deep Learning
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Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling.

PLoS computational biology Jun 24, 2024
As of now, more than 60 years have passed since the first determination of protein structures through crystallography, and a significant portion of protein structures can be predicted by computers. This is due to the groundbreaking enhancement in pro...
Humans Databases, Protein Deep Learning Protein Conformation Neural Networks, Computer Models, Molecular Antibodies Complementarity Determining Regions Computational Biology Algorithms
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Computational design of soluble and functional membrane protein analogues.

Nature Jun 19, 2024
De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topolog...
Amino Acid Motifs Proof of Concept Study Protein Folding Membrane Proteins Receptors, G-Protein-Coupled Deep Learning Solubility Proteome Protein Stability Humans Computer-Aided Design Models, Molecular
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Highly accurate carbohydrate-binding site prediction with DeepGlycanSite.

Nature communications Jun 17, 2024
As the most abundant organic substances in nature, carbohydrates are essential for life. Understanding how carbohydrates regulate proteins in the physiological and pathological processes presents opportunities to address crucial biological problems a...
Proteins Models, Molecular Binding Sites Carbohydrates Humans Deep Learning Neural Networks, Computer Protein Binding
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EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks.

International journal of molecular sciences Jun 6, 2024
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 ...
Neural Networks, Computer Models, Molecular Protein Conformation Protein Multimerization Computational Biology Proteins
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