AIMC Topic: Protein Structure, Secondary

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All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

Proceedings of the National Academy of Sciences of the United States of America
Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-hel...

Types and effects of protein variations.

Human genetics
Variations in proteins have very large number of diverse effects affecting sequence, structure, stability, interactions, activity, abundance and other properties. Although protein-coding exons cover just over 1 % of the human genome they harbor an di...

Prediction of β-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine.

Journal of theoretical biology
β-Lactam class of antibiotics is used as major therapeutic agent against a number of pathogenic microbes. The widespread and indiscriminate use of antibiotics to treat bacterial infection has prompted evolution of several evading mechanisms from the ...

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

IEEE/ACM transactions on computational biology and bioinformatics
Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous metho...

DCBLSTM-Deep Convolutional Bidirectional Long Short-Term Memory neural network for Q8 secondary protein structure prediction.

Computers in biology and medicine
Protein secondary structure prediction involves determining a protein's secondary structure from its primary amino acid sequence, serving as a critical step toward tertiary structure prediction. This, in turn, is essential for applications in drug de...

DSSP 4: FAIR annotation of protein secondary structure.

Protein science : a publication of the Protein Society
Protein secondary structure annotation is essential for understanding protein architecture, serving as a cornerstone for structural classification, alignment, visualization, and machine learning applications. The Define Secondary Structure of Protein...

Machine learning enabled protein secondary structure characterization using drop-coating deposition Raman spectroscopy.

Journal of pharmaceutical and biomedical analysis
Protein structure characterization is critical for therapeutic protein drug development and production. Drop-coating deposition Raman (DCDR) spectroscopy offers rapid and cost-effective acquisition of vibrational spectral data characteristic of prote...

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

Biomaterials science
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 ...

DeepSS2GO: protein function prediction from secondary structure.

Briefings in bioinformatics
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...

Multi-indicator comparative evaluation for deep learning-based protein sequence design methods.

Bioinformatics (Oxford, England)
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...