AIMC Topic: Amino Acid Sequence

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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 ...
Protein Structure, Secondary Amino Acid Sequence Algorithms Amino Acids Proteins Neural Networks, Computer
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MLapRVFL: Protein sequence prediction based on Multi-Laplacian Regularized Random Vector Functional Link.

Computers in biology and medicine Oct 26, 2023
Protein sequence classification is a crucial research field in bioinformatics, playing a vital role in facilitating functional annotation, structure prediction, and gaining a deeper understanding of protein function and interactions. With the rapid d...
Algorithms Amino Acid Sequence Proteins Machine Learning
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PortPred: Exploiting deep learning embeddings of amino acid sequences for the identification of transporter proteins and their substrates.

Journal of cellular biochemistry Oct 25, 2023
The physiology of every living cell is regulated at some level by transporter proteins which constitute a relevant portion of membrane-bound proteins and are involved in the movement of ions, small and macromolecules across bio-membranes. The importa...
Amino Acid Sequence Membrane Proteins Membrane Transport Proteins Deep Learning Computational Biology Machine Learning
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Integrating Pre-Trained protein language model and multiple window scanning deep learning networks for accurate identification of secondary active transporters in membrane proteins.

Methods (San Diego, Calif.) Oct 21, 2023
Secondary active transporters play pivotal roles in regulating ion and molecule transport across cell membranes, with implications in diseases like cancer. However, studying transporters via biochemical experiments poses challenges. We propose an eff...
Amino Acid Sequence Deep Learning Membrane Proteins Machine Learning Neural Networks, Computer
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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...
Neural Networks, Computer Amino Acid Sequence Protein Structure, Secondary Proteins Deep Learning
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Prediction of Protein-Protein Interactions Using Vision Transformer and Language Model.

IEEE/ACM transactions on computational biology and bioinformatics Oct 9, 2023
The knowledge of protein-protein interaction (PPI) helps us to understand proteins' functions, the causes and growth of several diseases, and can aid in designing new drugs. The majority of existing PPI research has relied mainly on sequence-based ap...
Multiomics Proteins Neural Networks, Computer Humans Amino Acid Sequence Saccharomyces cerevisiae
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SeqPredNN: a neural network that generates protein sequences that fold into specified tertiary structures.

BMC bioinformatics Oct 3, 2023
BACKGROUND: The relationship between the sequence of a protein, its structure, and the resulting connection between its structure and function, is a foundational principle in biological science. Only recently has the computational prediction of prote...
Amino Acid Sequence Protein Folding Amino Acids Proteins Neural Networks, Computer
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Empowering peptidomics: utilizing computational tools and approaches.

Bioanalysis Sep 22, 2023
Bioinformatics plays a critical role in the advancement of peptidomics by providing powerful tools for data analysis, interpretation and integration. Peptidomics is concerned with the study of peptides, short chains of amino acids with diverse biolog...
Peptides Computational Biology Power, Psychological Artificial Intelligence Amino Acid Sequence
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Drug-target binding affinity prediction using message passing neural network and self supervised learning.

BMC genomics Sep 20, 2023
BACKGROUND: Drug-target binding affinity (DTA) prediction is important for the rapid development of drug discovery. Compared to traditional methods, deep learning methods provide a new way for DTA prediction to achieve good performance without much k...
Amino Acid Sequence Neural Networks, Computer Supervised Machine Learning Drug Discovery
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Prediction of hot spots towards drug discovery by protein sequence embedding with 1D convolutional neural network.

PloS one Sep 18, 2023
Protein hotspot residues are key sites that mediate protein-protein interactions. Accurate identification of these residues is essential for understanding the mechanism from protein to function and for designing drug targets. Current research has mos...
Amino Acids Algorithms Neural Networks, Computer Amino Acid Sequence Drug Discovery
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