AIMC Topic: Protein Conformation

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Artificial Intelligence: A New Tool for Structure-Based G Protein-Coupled Receptor Drug Discovery.

Biomolecules Mar 17, 2025
Understanding protein structures can facilitate the development of therapeutic drugs. Traditionally, protein structures have been determined through experimental approaches such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy...
Drug Discovery Computational Biology Ligands Protein Conformation Artificial Intelligence Receptors, G-Protein-Coupled Humans Algorithms Molecular Docking Simulation
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Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis.

Journal of chemical theory and computation Mar 13, 2025
Protein evolution has shaped enzymes that maintain stability and function across diverse thermal environments. While sequence variation, thermal stability and conformational dynamics are known to influence an enzyme's thermal adaptation, how these fa...
Enzyme Stability Protein Conformation Malate Dehydrogenase Cytosol Evolution, Molecular Molecular Dynamics Simulation Temperature Deep Learning
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Machine learning methods to study sequence-ensemble-function relationships in disordered proteins.

Current opinion in structural biology Mar 12, 2025
Recent years have seen tremendous developments in the use of machine learning models to link amino-acid sequence, structure, and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and sequences th...
Models, Molecular Amino Acid Sequence Intrinsically Disordered Proteins Machine Learning Computational Biology Protein Conformation Protein Folding Humans
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Enhancing Functional Protein Design Using Heuristic Optimization and Deep Learning for Anti-Inflammatory and Gene Therapy Applications.

Proteins Feb 22, 2025
Protein sequence design is a highly challenging task, aimed at discovering new proteins that are more functional and producible under laboratory conditions than their natural counterparts. Deep learning-based approaches developed to address this prob...
Humans Algorithms Deep Learning Protein Conformation Genetic Therapy Protein Engineering Anti-Inflammatory Agents Amino Acid Sequence Heuristics Proteins Models, Molecular
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Teaching AI to speak protein.

Current opinion in structural biology Feb 21, 2025
Large Language Models for proteins, namely protein Language Models (pLMs), have begun to provide an important alternative to capturing the information encoded in a protein sequence in computers. Arguably, pLMs have advanced importantly to understandi...
Models, Molecular Protein Conformation Humans Artificial Intelligence Computational Biology Proteins
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Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning.

Journal of chemical information and modeling Feb 21, 2025
Proteins are inherently dynamic, and their conformational ensembles play a crucial role in biological function. Large-scale motions may govern the protein structure-function relationship, and numerous transient but stable conformations of intrinsical...
Protein Conformation Molecular Dynamics Simulation Intrinsically Disordered Proteins Amyloid beta-Peptides Deep Learning Peptide Fragments
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Toward deep learning sequence-structure co-generation for protein design.

Current opinion in structural biology Feb 20, 2025
Deep generative models that learn from the distribution of natural protein sequences and structures may enable the design of new proteins with valuable functions. While the majority of today's models focus on generating either sequences or structures...
Deep Learning Proteins Protein Engineering Models, Molecular Protein Conformation
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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 Feb 14, 2025
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...
Peptides Density Functional Theory Electrons Protein Conformation Molecular Dynamics Simulation Machine Learning Protein Multimerization
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AI protocol for retrieving protein dynamic structures from two-dimensional infrared spectra.

Proceedings of the National Academy of Sciences of the United States of America Feb 14, 2025
Understanding the dynamic evolution of protein structures is crucial for uncovering their biological functions. Yet, real-time prediction of these dynamic structures remains a significant challenge. Two-dimensional infrared (2DIR) spectroscopy is a p...
Protein Folding Protein Conformation Spectrophotometry, Infrared Machine Learning Proteins
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Simpler Protein Domain Identification Using Spectral Clustering.

Proteins Feb 13, 2025
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spect...
Proteins Algorithms Databases, Protein Deep Learning Models, Molecular Protein Conformation Computational Biology Protein Domains Sequence Alignment Cluster Analysis Amino Acid Sequence Sequence Analysis, Protein
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