AIMC Topic: Amino Acid Motifs

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MDD-SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs.

Bioinformatics (Oxford, England) Sep 26, 2015
UNLABELLED: S-sulfenylation (S-sulphenylation, or sulfenic acid), the covalent attachment of S-hydroxyl (-SOH) to cysteine thiol, plays a significant role in redox regulation of protein functions. Although sulfenic acid is transient and labile, most ...
Humans Sequence Analysis, Protein Software Sulfur Acids Support Vector Machine Cysteine Protein Processing, Post-Translational Proteins Amino Acid Motifs Amino Acids
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jEcho: an Evolved weight vector to CHaracterize the protein's posttranslational modification mOtifs.

Interdisciplinary sciences, computational life sciences Aug 6, 2015
Protein's posttranslational modification (PTM) represents a major dynamic regulation of protein functions after the translation of polypeptide chains from mRNA molecule. Compared with the costly and labor-intensive wet laboratory characterization of ...
Software Design Amino Acid Motifs Phosphorylation Data Mining Protein Processing, Post-Translational Databases, Protein Support Vector Machine
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PLPTP: A Motif-based Interpretable Deep Learning Framework Based on Protein Language Models for Peptide Toxicity Prediction.

Journal of molecular biology Jun 15, 2025
Peptide toxicity prediction holds significant importance in drug development and biotechnology, as accurately identifying toxic peptide sequences is crucial for designing safer peptide-based drugs. This study proposes a deep learning-based model for ...
Peptides Amino Acid Sequence Deep Learning Amino Acid Motifs Humans Computational Biology Neural Networks, Computer Proteins
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ScanNet uncovers binding motifs in protein structures with deep learning.

Nature methods Jun 1, 2022
Protein Binding Binding Sites Nucleotide Motifs Amino Acid Motifs Deep Learning
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Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network.

Briefings in bioinformatics Nov 5, 2021
Motif identification is among the most common and essential computational tasks for bioinformatics and genomics. Here we proposed a novel convolutional layer for deep neural network, named variable convolutional (vConv) layer, for effective motif ide...
Software Algorithms Humans Neural Networks, Computer Computational Biology Benchmarking Deep Learning Genomics Amino Acid Motifs High-Throughput Nucleotide Sequencing Nucleotide Motifs
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Locating transcription factor binding sites by fully convolutional neural network.

Briefings in bioinformatics Sep 2, 2021
Transcription factors (TFs) play an important role in regulating gene expression, thus identification of the regions bound by them has become a fundamental step for molecular and cellular biology. In recent years, an increasing number of deep learnin...
Amino Acid Motifs Sequence Analysis, Protein Response Elements Chromatin Immunoprecipitation Sequencing MCF-7 Cells A549 Cells Humans Transcription Factors Neural Networks, Computer Sequence Analysis, DNA
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Computer-Aided Virtual Screening and Designing of Cell-Penetrating Peptides.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2015
Cell-penetrating peptides (CPPs) have proven their potential as versatile drug delivery vehicles. Last decade has witnessed an unprecedented growth in CPP-based research, demonstrating the potential of CPPs as therapeutic candidates. In the past, man...
Cell-Penetrating Peptides Molecular Sequence Data Proteins Amino Acid Sequence Amino Acid Motifs Animals Machine Learning Support Vector Machine Computer-Aided Design Computer Simulation Drug Carriers Humans
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