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Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences.
Brief Bioinform
November 2024
Department of Computer Science, Virginia Commonwealth University, 401 West Main Street, Richmond, VA 23284, United States.
Computational prediction of nucleic acid-binding residues in protein sequences is an active field of research, with over 80 methods that were released in the past 2 decades. We identify and discuss 87 sequence-based predictors that include dozens of recently published methods that are surveyed for the first time. We overview historical progress and examine multiple practical issues that include availability and impact of predictors, key features of their predictive models, and important aspects related to their training and assessment.
View Article and Find Full Text PDFSProtFP: a machine learning-based method for functional classification of small ORFs in prokaryotes.
NAR Genom Bioinform
March 2025
National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
Small proteins (≤100 amino acids) play important roles across all life forms, ranging from unicellular bacteria to higher organisms. In this study, we have developed SProtFP which is a machine learning-based method for functional annotation of prokaryotic small proteins into selected functional categories. SProtFP uses independent artificial neural networks (ANNs) trained using a combination of physicochemical descriptors for classifying small proteins into antitoxin type 2, bacteriocin, DNA-binding, metal-binding, ribosomal protein, RNA-binding, type 1 toxin and type 2 toxin proteins.
View Article and Find Full Text PDFmiR-122/NEGR1 axis contributes colorectal cancer liver metastasis by PI3K/AKT pathway and macrophage modulation.
J Transl Med
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Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China.
Colorectal cancer (CRC) is a prevalent malignant tumor in the gastrointestinal tract, with around 50% of patients experiencing distant metastases, predominantly to the liver. Colorectal cancer liver metastasis (CRLM) is a leading cause of CRC-related death, and effective treatments remain limited. This study aims to identify new targets for predicting and treating CRLM.
View Article and Find Full Text PDFSubgenomic flaviviral RNAs and human proteins: exploration of anti-host defense mechanisms.
Comput Struct Biotechnol J
December 2024
Centre for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, Genova GE 16152, Italy.
Flaviviruses pose significant global health threats, infecting over 300 million people annually. Among their evasion strategies, the production of subgenomic flaviviral RNAs (sfRNAs) from the 3' UTR of viral genomes is particularly notable. Utilizing a comprehensive approach with the RAPID algorithm, we analyzed over 300,000 interactions between sfRNAs and human proteins derived from more than 8000 flavivirus genomes, including Dengue, Zika, Yellow Fever, West Nile, and Japanese Encephalitis viruses.
View Article and Find Full Text PDFInvestigation of RNA-binding protein NOVA1 in silico: Comparison of the modern human V197 with the archaic I197 variant present in Neanderthals.
Comput Biol Med
December 2024
Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; yΘμ Study Group, ProspED Polytechnic, Carlton, VIC, 3053, Australia; Baker Department of Cardiometabolic Health, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia. Electronic address:
Article Synopsis
- Researchers have identified specific genetic differences between archaic and modern human genomes, notably a switch in the NOVA1 gene linked to RNA regulation in neurons, changing an amino acid from isoleucine to valine.
- Using advanced modeling techniques, they compared the structures and binding interactions of the archaic and modern NOVA1 variants, finding similar binding free energies for protein-RNA complexes.
- The study suggests that although structural changes are modest, more research is needed to understand how mutations in NOVA1 affect alternative splicing and contribute to diseases, especially considering the roles of multiple mutations.
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