AIMC Topic: Protein Structure, Secondary

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ProSTAGE: Predicting Effects of Mutations on Protein Stability by Using Protein Embeddings and Graph Convolutional Networks.

Journal of chemical information and modeling Jan 2, 2024
Protein thermodynamic stability is essential to clarify the relationships among structure, function, and interaction. Therefore, developing a faster and more accurate method to predict the impact of the mutations on protein stability is helpful for p...
Neural Networks, Computer Protein Stability Protein Structure, Secondary Proteins Mutation
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De novo design of high-affinity binders of bioactive helical peptides.

Nature Dec 18, 2023
Many peptide hormones form an α-helix on binding their receptors, and sensitive methods for their detection could contribute to better clinical management of disease. De novo protein design can now generate binders with high affinity and specificity ...
Computer-Aided Design Deep Learning Peptides Glucagon Substrate Specificity Protein Structure, Secondary Models, Molecular Luminescent Measurements Mass Spectrometry Diffusion Biosensing Techniques Proteins Parathyroid Hormone
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Effective Local and Secondary Protein Structure Prediction by Combining a Neural Network-Based Approach with Extensive Feature Design and Selection without Reliance on Evolutionary Information.

International journal of molecular sciences Oct 27, 2023
Protein structure prediction continues to pose multiple challenges despite outstanding progress that is largely attributable to the use of novel machine learning techniques. One of the widely used representations of local 3D structure-protein blocks ...
Proteins Amino Acids Amino Acid Sequence Protein Structure, Secondary Neural Networks, Computer Algorithms
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Naive Prediction of Protein Backbone Phi and Psi Dihedral Angles Using Deep Learning.

Molecules (Basel, Switzerland) Oct 12, 2023
Protein structure prediction represents a significant challenge in the field of bioinformatics, with the prediction of protein structures using backbone dihedral angles recently achieving significant progress due to the rise of deep neural network re...
Proteins Amino Acid Sequence Neural Networks, Computer Deep Learning Protein Structure, Secondary
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More than just pattern recognition: Prediction of uncommon protein structure features by AI methods.

Proceedings of the National Academy of Sciences of the United States of America Jul 3, 2023
The CASP14 experiment demonstrated the extraordinary structure modeling capabilities of artificial intelligence (AI) methods. That result has ignited a fierce debate about what these methods are actually doing. One of the criticisms has been that the...
Protein Structure, Secondary Artificial Intelligence Proteins Amino Acid Sequence Protein Conformation Neural Networks, Computer
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Mathematical and Machine Learning Approaches for Classification of Protein Secondary Structure Elements from Coordinates.

Biomolecules May 31, 2023
Determining Secondary Structure Elements (SSEs) for any protein is crucial as an intermediate step for experimental tertiary structure determination. SSEs are identified using popular tools such as DSSP and STRIDE. These tools use atomic information ...
Machine Learning Algorithms Protein Structure, Secondary Proteins Hydrogen Bonding
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Sequence similarity governs generalizability of de novo deep learning models for RNA secondary structure prediction.

PLoS computational biology Apr 17, 2023
Making no use of physical laws or co-evolutionary information, de novo deep learning (DL) models for RNA secondary structure prediction have achieved far superior performances than traditional algorithms. However, their statistical underpinning raise...
RNA Protein Structure, Secondary Machine Learning Algorithms Deep Learning
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RNA independent fragment partition method based on deep learning for RNA secondary structure prediction.

Scientific reports Feb 17, 2023
The non-coding RNA secondary structure largely determines its function. Hence, accuracy in structure acquisition is of great importance. Currently, this acquisition primarily relies on various computational methods. The prediction of the structures o...
Algorithms Deep Learning Nucleic Acid Conformation Protein Structure, Secondary Computational Biology RNA
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Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-Based Cube-Format Feature.

IEEE/ACM transactions on computational biology and bioinformatics Dec 8, 2022
Protein-DNA interactions play an important role in diverse biological processes. Accurately identifying protein-DNA binding residues is a critical but challenging task for protein function annotations and drug design. Although wet-lab experimental me...
DNA Protein Binding Neural Networks, Computer Protein Structure, Secondary Proteins
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Convolutional ProteinUnetLM competitive with long short-term memory-based protein secondary structure predictors.

Proteins Dec 5, 2022
The protein secondary structure (SS) prediction plays an important role in the characterization of general protein structure and function. In recent years, a new generation of algorithms for SS prediction based on embeddings from protein language mod...
Proteins Protein Structure, Secondary Neural Networks, Computer Algorithms
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