AIMC Topic: Protein Structure, Secondary

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Machine-learning-guided identification of protein secondary structures using spectral and structural descriptors.

Biomaterials science May 27, 2025
Interrogation of the secondary structures of proteins is essential for designing and engineering more effective and safer protein-based biomaterials and other classes of theranostic materials. Protein secondary structures are commonly assessed using ...
Machine Learning Protein Structure, Secondary Algorithms Circular Dichroism Proteins
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DeepSS2GO: protein function prediction from secondary structure.

Briefings in bioinformatics Mar 27, 2024
Predicting protein function is crucial for understanding biological life processes, preventing diseases and developing new drug targets. In recent years, methods based on sequence, structure and biological networks for protein function annotation hav...
Sequence Analysis, Protein Algorithms Gene Ontology Computational Biology Protein Structure, Secondary Proteins Neural Networks, Computer Software Databases, Protein
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Multi-indicator comparative evaluation for deep learning-based protein sequence design methods.

Bioinformatics (Oxford, England) Feb 1, 2024
MOTIVATION: Proteins found in nature represent only a fraction of the vast space of possible proteins. Protein design presents an opportunity to explore and expand this protein landscape. Within protein design, protein sequence design plays a crucial...
Proteins Amino Acids Deep Learning Amino Acid Sequence Protein Structure, Secondary
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AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences.

Nucleic acids research Jan 5, 2024
The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expanding from the initial 300k structures released...
Amino Acid Sequence Protein Structure, Secondary Proteins Databases, Protein Search Engine Artificial Intelligence Proteome
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HN-PPISP: a hybrid network based on MLP-Mixer for protein-protein interaction site prediction.

Briefings in bioinformatics Jan 19, 2023
MOTIVATION: Biological experimental approaches to protein-protein interaction (PPI) site prediction are critical for understanding the mechanisms of biochemical processes but are time-consuming and laborious. With the development of Deep Learning (DL...
Amino Acid Sequence Protein Structure, Secondary Software Amino Acids Neural Networks, Computer
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HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures.

Bioinformatics (Oxford, England) Jan 1, 2023
MOTIVATION: Protein and peptide engineering has become an essential field in biomedicine with therapeutics, diagnostics and synthetic biology applications. Helices are both abundant structural feature in proteins and comprise a major portion of bioac...
Peptides Deep Learning Proteins Protein Structure, Secondary Protein Conformation, alpha-Helical
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LambdaPP: Fast and accessible protein-specific phenotype predictions.

Protein science : a publication of the Protein Society Jan 1, 2023
The availability of accurate and fast artificial intelligence (AI) solutions predicting aspects of proteins are revolutionizing experimental and computational molecular biology. The webserver LambdaPP aspires to supersede PredictProtein, the first in...
Artificial Intelligence Proteins Protein Structure, Secondary Amino Acid Sequence Software Sequence Alignment
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GeoPacker: A novel deep learning framework for protein side-chain modeling.

Protein science : a publication of the Protein Society Dec 1, 2022
Atomic interactions play essential roles in protein folding, structure stabilization, and function performance. Recent advances in deep learning-based methods have achieved impressive success not only in protein structure prediction, but also in prot...
Protein Structure, Secondary Amino Acid Sequence Protein Conformation Proteins Algorithms Deep Learning
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Deep learning models for RNA secondary structure prediction (probably) do not generalize across families.

Bioinformatics (Oxford, England) Aug 10, 2022
MOTIVATION: The secondary structure of RNA is of importance to its function. Over the last few years, several papers attempted to use machine learning to improve de novo RNA secondary structure prediction. Many of these papers report impressive resul...
Humans Machine Learning Neural Networks, Computer Deep Learning RNA Protein Structure, Secondary
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Prior knowledge facilitates low homologous protein secondary structure prediction with DSM distillation.

Bioinformatics (Oxford, England) Jul 11, 2022
MOTIVATION: Protein secondary structure prediction (PSSP) is one of the fundamental and challenging problems in the field of computational biology. Accurate PSSP relies on sufficient homologous protein sequences to build the multiple sequence alignme...
Proteins Neural Networks, Computer Humans Sequence Alignment Protein Structure, Secondary Computational Biology Position-Specific Scoring Matrices
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