Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences DOI Creative Commons
Sushmita Basu, Jing Yu, Daisuke Kihara

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 26(1)

Published: Nov. 22, 2024

Abstract Computational prediction of nucleic acid-binding residues in protein sequences is an active field research, with over 80 methods that were released the past 2 decades. We identify and discuss 87 sequence-based predictors include dozens recently published are surveyed for first time. overview historical progress examine multiple practical issues availability impact predictors, key features their predictive models, important aspects related to training assessment. observe decade has brought increased use deep neural networks language which contributed substantial gains performance. also highlight advancements vital challenging cross-predictions between deoxyribonucleic acid (DNA)-binding ribonucleic (RNA)-binding targeting two distinct sources binding annotations, structure-based versus intrinsic disorder-based. The trained on structure-annotated interactions tend perform poorly disorder-annotated vice versa, only a few target well across both annotation types. significant problem, some DNA-binding or RNA-binding indiscriminately predicting Moreover, we show web servers cited substantially more than tools without implementation no longer working implementations, motivating development long-term maintenance servers. close by discussing future research directions aim drive further this area.

Language: Английский

Merkel cell carcinoma: updates in tumor biology, emerging therapies, and preclinical models DOI Creative Commons
Elisabeth A. Pedersen, Monique Verhaegen,

Mallory Joseph

et al.

Frontiers in Oncology, Journal Year: 2024, Volume and Issue: 14

Published: July 29, 2024

Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine thought to arise via either viral (Merkel polyomavirus) or ultraviolet-associated pathways. Surgery and radiotherapy have historically been mainstays of management, immunotherapy has improved outcomes for advanced disease. However, there remains a lack effective therapy those patients who fail respond these established approaches, underscoring critical need better understand MCC biology more prognosis treatment. Here, we review the fundamental aspects recent advances which had profound impact on management. The first genetically-engineered mouse models tumorigenesis provide opportunities potential origin may prove useful preclinical investigation novel therapeutics. debate also by observations arising in association with clonally related hair follicle tumor squamous

Language: Английский

Citations

2
Introduction: The Role of Pathogens Associated with Human Cancer and the Concept of Omics–An Overview DOI
Noé Velázquez-Márquez,

Laura Cristina Huelgas-Saavedra

Published: Jan. 1, 2024

Language: Английский

Citations

0
Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences DOI Creative Commons
Sushmita Basu, Jing Yu, Daisuke Kihara

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 26(1)

Published: Nov. 22, 2024

Abstract Computational prediction of nucleic acid-binding residues in protein sequences is an active field research, with over 80 methods that were released the past 2 decades. We identify and discuss 87 sequence-based predictors include dozens recently published are surveyed for first time. overview historical progress examine multiple practical issues availability impact predictors, key features their predictive models, important aspects related to training assessment. observe decade has brought increased use deep neural networks language which contributed substantial gains performance. also highlight advancements vital challenging cross-predictions between deoxyribonucleic acid (DNA)-binding ribonucleic (RNA)-binding targeting two distinct sources binding annotations, structure-based versus intrinsic disorder-based. The trained on structure-annotated interactions tend perform poorly disorder-annotated vice versa, only a few target well across both annotation types. significant problem, some DNA-binding or RNA-binding indiscriminately predicting Moreover, we show web servers cited substantially more than tools without implementation no longer working implementations, motivating development long-term maintenance servers. close by discussing future research directions aim drive further this area.

Language: Английский

Citations

0