Protein Function Prediction from Protein-Protein Interaction Network (PPIN) and physico-chemical features using the Gene Ontology (GO) classification are indeed very useful for assigning biological or biochemical functions to a protein. They also lead to the identification of those significant proteins which are responsible for the generation of various diseases whose drugs are still yet to be discovered. So, the prediction of GO functional terms from PPIN and sequence is an important field of study. In this work, we have proposed a methodology, Multi Label Protein Function Prediction (ML_PFP) which is based on Neighborhood analysis empowered with physico-chemical features of constituent amino acids to predict the functional group of unannotated protein. A protein does not perform functions in isolation rather it performs functions in a group by interacting with others. So a protein is involved in many functions or, in other words, may be associated with multiple functional groups or labels or GO terms. Though functional group of other known interacting partner protein and its physico-chemical features provide useful information, assignment of multiple labels to unannotated protein is a very challenging task. Here, we have taken Homo sapiens or Human PPIN as well as Saccharomyces cerevisiae or yeast PPIN along with their GO terms to predict functional groups or GO terms of unannotated proteins. This work has become very challenging as both Human and Yeast protein dataset are voluminous and complex in nature and multi-label functional groups assignment has also added a new dimension to this challenge. Our algorithm has been observed to achieve a better performance in Cellular Function, Molecular Function and Biological Process of both yeast and human network when compared with the other existing state-of-the-art methodologies which will be discussed in detail in the results section.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1142/S0219720018500257 | DOI Listing |
Phys Chem Chem Phys
January 2025
Department of Science Education, Graduate School of Humanities and Social Sciences, Hiroshima University, 1-1-1 Kagamiyama, Higashi-Hiroshima 739-8524, Japan.
The thermal dehydration of sodium carbonate monohydrate (SC-MH) exhibits kinetic characteristics that are typical of the thermal decomposition of solids with a reversible nature. One of the characteristics is the physico-geometrical constraints of the reaction due to the heterogeneous reaction feature. Another factor is the considerable impact of the atmospheric and self-generated water vapor on the kinetics.
View Article and Find Full Text PDFBiochimie
January 2025
Laboratory of Antimicrobial Resistance, Institute of Ecological and Agricultural Biology (X-BIO), Tyumen State University, Tyumen, Russia.
Macrolactin A (McA) is a secondary metabolite produced by Bacillus species. It has been known for its antimicrobial properties since the late 1980s, although the exact mechanism of its antibacterial activity remains unknown. In this study, we have found that McA is an inhibitor of protein synthesis in bacteria.
View Article and Find Full Text PDFPlants (Basel)
December 2024
A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia.
Among the long non-coding RNAs that are currently recognized as important regulatory molecules influencing a plethora of processes in eukaryotic cells, circular RNAs (circRNAs) represent a distinct class of RNAs that are predominantly produced by back-splicing of pre-mRNA. The most studied regulatory mechanisms involving circRNAs are acting as miRNA sponges, forming R-loops with genomic DNA, and encoding functional proteins. In addition to circRNAs generated by back-splicing, two types of circRNAs capable of autonomous RNA-RNA replication and systemic transport have been described in plants: viroids, which are infectious RNAs that cause a number of plant diseases, and retrozymes, which are transcripts of retrotransposon genomic loci that are capable of circularization due to ribozymes.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Chemistry Department, Lomonosov Moscow State University, Moscow 119991, Russia.
Non-canonical nucleic acid structures play significant roles in cellular processes through selective interactions with proteins. While both natural and artificial G-quadruplexes have been extensively studied, the functions of i-motifs remain less understood. This study investigates the artificial aptamer BV42, which binds strongly to influenza A virus hemagglutinin and unexpectedly retains its i-motif structure even at neutral pH.
View Article and Find Full Text PDFGenes (Basel)
December 2024
Research Centre for Medical Genetics, 1 Moskvorechye St., 115522 Moscow, Russia.
Introduction: Pathogenic variants in the gene are linked to a spectrum of syndromes that exhibit partial clinical overlap. Hemizygous loss-of-function variants are considered lethal in males, while heterozygous loss-of-function variants generally result in oro-facial-digital syndrome type 1. A reported phenotype, Simpson-Golabi-Behmel syndrome type 2, was published once but remains controversial, with many specialists questioning its validity and arguing about its continued listing in the OMIM database.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!