AIMC Topic: Protein Conformation

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ALDELE: All-Purpose Deep Learning Toolkits for Predicting the Biocatalytic Activities of Enzymes.

Journal of chemical information and modeling Apr 4, 2024
Rapidly predicting enzyme properties for catalyzing specific substrates is essential for identifying potential enzymes for industrial transformations. The demand for sustainable production of valuable industry chemicals utilizing biological resources...
Biocatalysis Protein Conformation Enzymes Deep Learning Models, Molecular
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FuncPhos-STR: An integrated deep neural network for functional phosphosite prediction based on AlphaFold protein structure and dynamics.

International journal of biological macromolecules Mar 27, 2024
Phosphorylation modifications play important regulatory roles in most biological processes. However, the functional assignment for the vast majority of the identified phosphosites remains a major challenge. Here, we provide a deep learning framework ...
Software Deep Learning Proteins Protein Conformation Computational Biology Humans Neural Networks, Computer
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Prediction of order parameters based on protein NMR structure ensemble and machine learning.

Journal of biomolecular NMR Mar 26, 2024
The fast motions of proteins at the picosecond to nanosecond timescale, known as fast dynamics, are closely related to protein conformational entropy and rearrangement, which in turn affect catalysis, ligand binding and protein allosteric effects. Th...
Protein Conformation Nuclear Magnetic Resonance, Biomolecular Machine Learning Proteins
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A suite of designed protein cages using machine learning and protein fragment-based protocols.

Structure (London, England : 1993) Mar 20, 2024
Designed protein cages and related materials provide unique opportunities for applications in biotechnology and medicine, but their creation remains challenging. Here, we apply computational approaches to design a suite of tetrahedrally symmetric, se...
Proteins Models, Molecular Hydrophobic and Hydrophilic Interactions Machine Learning Molecular Docking Simulation Protein Conformation Cryoelectron Microscopy
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Flattening the curve-How to get better results with small deep-mutational-scanning datasets.

Proteins Mar 19, 2024
Proteins are used in various biotechnological applications, often requiring the optimization of protein properties by introducing specific amino-acid exchanges. Deep mutational scanning (DMS) is an effective high-throughput method for evaluating the ...
Mutation Protein Conformation Proteins Databases, Protein Machine Learning Software Deep Learning Computational Biology Algorithms Humans Neural Networks, Computer
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Epitope Identification of an mGlu5 Receptor Nanobody Using Physics-Based Molecular Modeling and Deep Learning Techniques.

Journal of chemical information and modeling Feb 29, 2024
The world has witnessed a revolution in therapeutics with the development of biological medicines such as antibodies and antibody fragments, notably nanobodies. These nanobodies possess unique characteristics including high specificity and modulatory...
Molecular Dynamics Simulation Protein Conformation Animals Deep Learning Models, Molecular Epitope Mapping Single-Domain Antibodies Rats Epitopes Receptor, Metabotropic Glutamate 5
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Investigating the ability of deep learning-based structure prediction to extrapolate and/or enrich the set of antibody CDR canonical forms.

Frontiers in immunology Feb 28, 2024
Deep learning models have been shown to accurately predict protein structure from sequence, allowing researchers to explore protein space from the structural viewpoint. In this paper we explore whether "novel" features, such as distinct loop conforma...
Complementarity Determining Regions Antibodies Deep Learning Protein Conformation Models, Molecular
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Automated model building and protein identification in cryo-EM maps.

Nature Feb 26, 2024
Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs. Here we present ModelAngelo, a machine-learning approa...
Protein Conformation Neural Networks, Computer Cryoelectron Microscopy Machine Learning Computer Graphics Amino Acid Sequence Proteins Markov Chains Models, Molecular
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Recent Progress of Protein Tertiary Structure Prediction.

Molecules (Basel, Switzerland) Feb 13, 2024
The prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades. Recently, the widespread integration of artificial intelligence (AI)...
Models, Molecular Protein Conformation Protein Folding Proteins Artificial Intelligence Databases, Protein Algorithms Software Computational Biology
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De novo design of cavity-containing proteins with a backbone-centered neural network energy function.

Structure (London, England : 1993) Feb 6, 2024
The design of small-molecule-binding proteins requires protein backbones that contain cavities. Previous design efforts were based on naturally occurring cavity-containing backbone architectures. Here, we designed diverse cavity-containing backbones ...
Models, Molecular Protein Conformation Neural Networks, Computer Proteins
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