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   Articles with "modification sites" as a keyword



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motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs

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recommendations! Published in 2019 at "PROTEOMICS"

DOI: 10.1002/pmic.201900245

Abstract: With an exponential growth in applications identifying protein post‐translational modifications via mass spectrometry, discovery and presentation of motifs surrounding those modification sites have become increasingly desirable. Despite a few tools being designed, there is still… read more here.

Keywords: modification sites; integrated web; motifer integrated; web software ... See more keywords

Assessment of susceptible chemical modification sites of trastuzumab and endogenous human immunoglobulins at physiological conditions

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recommendations! Published in 2018 at "Communications Biology"

DOI: 10.1038/s42003-018-0032-8

Abstract: The quality control testing of chemical degradations in the bio-pharmaceutical industry is currently under controversial debate. Here we have systematically applied in vitro and in vivo stress conditions to investigate the influence of protein degradation… read more here.

Keywords: chemical modification; degradation; modification sites; sites trastuzumab ... See more keywords
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iRNAD: a computational tool for identifying D modification sites in RNA sequence

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recommendations! Published in 2019 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btz358

Abstract: MOTIVATION Dihydrouridine (D) is a common RNA posttranscriptional modification found in eukaryotes, bacteria and a few archaea. The modification can promote the conformational flexibility of individual nucleotide bases. And its levels are increased in cancerous… read more here.

Keywords: modification sites; rna sequence; identifying modification; sites rna ... See more keywords

Discovering Consensus Regions for Interpretable Identification of RNA N6-Methyladenosine Modification Sites via Graph Contrastive Clustering

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recommendations! Published in 2024 at "IEEE Journal of Biomedical and Health Informatics"

DOI: 10.1109/jbhi.2024.3357979

Abstract: As a pivotal post-transcriptional modification of RNA, N6-methyladenosine (m6A) has a substantial influence on gene expression modulation and cellular fate determination. Although a variety of computational models have been developed to accurately identify potential m6A… read more here.

Keywords: m6a; consensus regions; modification sites; identification ... See more keywords

YModPred: an interpretable prediction method for multi-type RNA modification sites in S. cerevisiae based on deep learning

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recommendations! Published in 2025 at "BMC Biology"

DOI: 10.1186/s12915-025-02372-y

Abstract: RNA post-transcriptional modifications involve the addition of chemical groups to RNA molecules or alterations to their local structure. These modifications can change RNA base pairing, affect thermal stability, and influence RNA folding, thereby impacting alternative… read more here.

Keywords: deep learning; rna; modification sites; prediction ... See more keywords

MultiV_Nm: a prediction method for 2′-O-methylation sites based on multi-view features

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recommendations! Published in 2025 at "Frontiers in Genetics"

DOI: 10.3389/fgene.2025.1608490

Abstract: As a crucial class of chemical modifications, 2′-O-methylation modification (abbreviated as Nm) is widely distributed in various organisms and plays a very important role in normal cellular physiological activities and the occurrence and development of… read more here.

Keywords: multiv prediction; modification sites; prediction; view features ... See more keywords

Identification of D Modification Sites Using a Random Forest Model Based on Nucleotide Chemical Properties

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recommendations! Published in 2022 at "International Journal of Molecular Sciences"

DOI: 10.3390/ijms23063044

Abstract: Dihydrouridine (D) is an abundant post-transcriptional modification present in transfer RNA from eukaryotes, bacteria, and archaea. D has contributed to treatments for cancerous diseases. Therefore, the precise detection of D modification sites can enable further… read more here.

Keywords: modification; identification modification; nucleotide chemical; random forest ... See more keywords

ENet-6mA: Identification of 6mA Modification Sites in Plant Genomes Using ElasticNet and Neural Networks

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recommendations! Published in 2022 at "International Journal of Molecular Sciences"

DOI: 10.3390/ijms23158314

Abstract: N6-methyladenine (6mA) has been recognized as a key epigenetic alteration that affects a variety of biological activities. Precise prediction of 6mA modification sites is essential for understanding the logical consistency of biological activity. There are… read more here.

Keywords: enet 6ma; 6ma modification; plant genomes; modification sites ... See more keywords