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Protein Multimerization

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Integrating different approaches for the identification of new disruptors of HIV-1 capsid multimerization.

Biochemical and biophysical research communications 40239540
Human Immunodeficiency Virus (HIV) belongs to the Lentivirus genus, Retroviridae family, enveloped by a lipid bilayer within which the capsid protein encases the viral genome, reverse transcriptase, and integrase proteins, key components for viral re...
Anti-HIV Agents Capsid Capsid Proteins HIV Infections HIV-1 Humans Protein Multimerization
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Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule.

Biophysical journal 38160255
Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions tha...
Animals Drosophila Proteins Ions Kinesins Machine Learning Microtubules Molecular Dynamics Simulation Protein Binding Protein Multimerization Solvents Static Electricity Tubulin
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Inactive-enriched machine-learning models exploiting patent data improve structure-based virtual screening for PDL1 dimerizers.

Journal of advanced research 38280715
INTRODUCTION: Small-molecule Programmable Cell Death Protein 1/Programmable Death-Ligand 1 (PD1/PDL1) inhibition via PDL1 dimerization has the potential to lead to inexpensive drugs with better cancer patient outcomes and milder side effects. However...
B7-H1 Antigen Drug Design Humans Machine Learning Patents as Topic Programmed Cell Death 1 Receptor Protein Multimerization
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DeepSub: Utilizing Deep Learning for Predicting the Number of Subunits in Homo-Oligomeric Protein Complexes.

International journal of molecular sciences 38732022
The molecular weight (MW) of an enzyme is a critical parameter in enzyme-constrained models (ecModels). It is determined by two factors: the presence of subunits and the abundance of each subunit. Although the number of subunits (NS) can potentially ...
Animals Computational Biology Databases, Protein Deep Learning Humans Mice Protein Multimerization Protein Subunits
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Interface design of SARS-CoV-2 symmetrical nsp7 dimer and machine learning-guided nsp7 sequence prediction reveals physicochemical properties and hotspots for nsp7 stability, adaptation, and therapeutic design.

Physical chemistry chemical physics : PCCP 38686454
The COVID-19 pandemic, driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates a profound understanding of the virus and its lifecycle. As an RNA virus with high mutation rates, SARS-CoV-2 exhibits genetic variability lea...
Amino Acid Sequence Coronavirus RNA-Dependent RNA Polymerase COVID-19 Humans Machine Learning Mutation Protein Multimerization SARS-CoV-2 Viral Nonstructural Proteins
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Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane.

Journal of chemical theory and computation 38918177
The accurate calculation of equilibrium constants for protein-protein association is of fundamental importance to quantitative biology and remains an outstanding challenge for computational biophysics. Traditionally, equilibrium constants have been c...
Machine Learning Membrane Proteins Molecular Dynamics Simulation Protein Multimerization Thermodynamics
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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 38892437
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 ...
Computational Biology Models, Molecular Neural Networks, Computer Protein Conformation Protein Multimerization Proteins
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Binding and sensing diverse small molecules using shape-complementary pseudocycles.

Science (New York, N.Y.) 39024436
We describe an approach for designing high-affinity small molecule-binding proteins poised for downstream sensing. We use deep learning-generated pseudocycles with repeating structural units surrounding central binding pockets with widely varying sha...
Binding Sites Deep Learning Ligands Methotrexate Molecular Docking Simulation Nanopores Protein Binding Protein Multimerization Proteins Small Molecule Libraries Thyroxine
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A synthetic protein-level neural network in mammalian cells.

Science (New York, N.Y.) 39666795
Artificial neural networks provide a powerful paradigm for nonbiological information processing. To understand whether similar principles could enable computation within living cells, we combined de novo-designed protein heterodimers and engineered v...
Cell Death HEK293 Cells Humans Neural Networks, Computer Protein Engineering Protein Interaction Maps Protein Multimerization Proteolysis Recombinant Fusion Proteins Synthetic Biology Viral Proteases
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Dynamic Electronic Structure Fluctuations in the De Novo Peptide ACC-Dimer Revealed by First-Principles Theory and Machine Learning.

Journal of chemical information and modeling 39950947
Recent studies have reported long-range charge transport in peptide- and protein-based fibers and wires, rendering this class of materials as promising charge-conducting interfaces between biological systems and electronic devices. In the complex mol...
Density Functional Theory Electrons Machine Learning Molecular Dynamics Simulation Peptides Protein Conformation Protein Multimerization
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