AIMC Topic: Amino Acid Sequence

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AI, docking, and molecular dynamics to track the binding of structural peptides to different keratin models.

International journal of biological macromolecules
The present work shows a computational approach to assess the interactions of different nature-inspired peptides with hair keratin models. An updated keratin model was validated, and comparisons with previous models were traced, thereby highlighting ...

Cyclic peptide structure prediction and design using AlphaFold2.

Nature communications
Small cyclic peptides have gained significant traction as a therapeutic modality; however, the development of deep learning methods for accurately designing such peptides has been slow, mostly due to the lack of sufficiently large training sets. Here...

Machine learning models for predicting configuration of modified knuckle epitope peptides of BMP-2 protein using mesoscale simulation data.

Physical chemistry chemical physics : PCCP
The high doses of bone morphogenetic proteins (BMPs) cause undesired side effects in skeletal tissue regeneration. An alternative approach is to use the bioactive knuckle epitope domain of BMP-2 (BMP2-KEP) with an open-arm structure as part of the pr...

Dynamics and Machine Learning Reveal the Link between Tripeptide Sequences and Evaporation-Driven Material Properties.

Nano letters
Previous research showed that a peptide composed of three tyrosines (YYY) can turn into organic glass and cause strong adhesion between substrates via evaporation. However, the mechanisms of these processes remain unclear, and the exploration of appl...

Amino acid sequence-based IDR classification using ensemble machine learning and quantum neural networks.

Computational biology and chemistry
Biologically traditional methods, such as the Uversky plot, which rely on hydrophobicity and net charge, have inherent limitations in accurately distinguishing intrinsically disordered regions (IDRs) from ordered protein regions. To overcome these co...

Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network.

Cell
In humans, selective and promiscuous interactions between 46 secreted chemokine ligands and 23 cell surface chemokine receptors of the G-protein-coupled receptor (GPCR) family form a complex network to coordinate cell migration. While chemokines and ...

Neural network conditioned to produce thermophilic protein sequences can increase thermal stability.

Scientific reports
This work presents Neural Optimization for Melting-temperature Enabled by Leveraging Translation (NOMELT), a novel approach for designing and ranking high-temperature stable proteins using neural machine translation. The model, trained on over 4 mill...

Optimizing lipocalin sequence classification with ensemble deep learning models.

PloS one
Deep learning (DL) has become a powerful tool for the recognition and classification of biological sequences. However, conventional single-architecture models often struggle with suboptimal predictive performance and high computational costs. To addr...

In silico design of ankyrin repeat proteins that bind to the insulin-like growth factor type 1 receptor.

Journal of molecular graphics & modelling
Ankyrins are proteins widely distributed in nature that mediate protein‒protein interactions. Owing to their outstanding stability and ability to recognize targets, ankyrins have been used as therapeutic and diagnostic tools in several diseases, incl...

Grain protein function prediction based on improved FCN and bidirectional LSTM.

Food chemistry
With the development of high-throughput sequencing technologies, predicting grain protein function from amino acid sequences based on intelligent model has become one of the significant tasks in bioinformatics. The soybean, maize, indica, and japonic...