Atomistic molecular dynamics simulations of intrinsically disordered proteins

IF 6.1 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Current opinion in structural biology Pub Date : 2025-03-10 DOI:10.1016/j.sbi.2025.103029

Fidha Nazreen Kunnath Muhammedkutty , Matthew MacAinsh , Huan-Xiang Zhou

引用次数: 0

Abstract

Recent years have seen remarkable gains in the accuracy of atomistic molecular dynamics (MD) simulations of intrinsically disordered proteins (IDPs) and expansion in the types of calculated properties that can be directly compared with experimental measurements. These advances occurred due to the use of IDP-tested force fields and the porting of MD simulations to GPUs and other computational technologies. All-atom MD simulations are now explaining the sequence-dependent dynamics of IDPs; elucidating the mechanisms of their binding to other proteins, nucleic acids, and membranes; revealing the modes of drug action on them; and characterizing their phase separation. Artificial intelligence (AI) and machine learning (ML) are further expanding the reach of atomistic MD simulations.

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来源期刊

Current opinion in structural biology 生物-生化与分子生物学

CiteScore

12.20

自引率

2.90%

发文量

179

审稿时长

6-12 weeks

期刊介绍： Current Opinion in Structural Biology (COSB) aims to stimulate scientifically grounded, interdisciplinary, multi-scale debate and exchange of ideas. It contains polished, concise and timely reviews and opinions, with particular emphasis on those articles published in the past two years. In addition to describing recent trends, the authors are encouraged to give their subjective opinion of the topics discussed. In COSB, we help the reader by providing in a systematic manner: 1. The views of experts on current advances in their field in a clear and readable form. 2. Evaluations of the most interesting papers, annotated by experts, from the great wealth of original publications. [...] The subject of Structural Biology is divided into twelve themed sections, each of which is reviewed once a year. Each issue contains two sections, and the amount of space devoted to each section is related to its importance. -Folding and Binding- Nucleic acids and their protein complexes- Macromolecular Machines- Theory and Simulation- Sequences and Topology- New constructs and expression of proteins- Membranes- Engineering and Design- Carbohydrate-protein interactions and glycosylation- Biophysical and molecular biological methods- Multi-protein assemblies in signalling- Catalysis and Regulation