IPAMD: A Plugin-Based Software for Biomolecular Condensate Simulations DOI
Xiaoyang Liu, You‐Liang Zhu, Yuze Jiang

et al.

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: May 27, 2025

The study of intrinsically disordered proteins (IDPs) and their role in biomolecular condensate formation has become a critical area research, offering insights into fundamental biological processes therapeutic development. Here, we present IPAMD (Intrinsically Protein Aggregation Molecular Dynamics), plugin-based software designed to simulate the dynamics condensates IDPs. provides modular, efficient, customizable simulation platform specifically for studies. It incorporates advanced force fields, such as HPS-based Mpipi models, employs optimization techniques large-scale simulations. features user-friendly interface supports batch processing, making it accessible researchers with varying computational expertise. Benchmarking case studies demonstrate ability accurately analyze structures properties.

Language: Английский

AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models DOI Creative Commons
Mátyás Pajkos,

Ilinka Clerc,

Christophe Zanon

et al.

Journal of Molecular Biology, Journal Year: 2025, Volume and Issue: unknown, P. 169003 - 169003

Published: Feb. 1, 2025

Language: Английский

Citations

2
Machine learning methods to study sequence–ensemble–function relationships in disordered proteins DOI Creative Commons
Sören von Bülow, Giulio Tesei, Kresten Lindorff‐Larsen

et al.

Current Opinion in Structural Biology, Journal Year: 2025, Volume and Issue: 92, P. 103028 - 103028

Published: March 12, 2025

Language: Английский

Citations

1
Modern machine learning methods for protein property prediction DOI

Arjun Dosajh,

P. K. Agrawal,

Prathit Chatterjee

et al.

Current Opinion in Structural Biology, Journal Year: 2025, Volume and Issue: 90, P. 102990 - 102990

Published: Jan. 28, 2025

Language: Английский

Citations

0
Salts Influence IDP Properties by Modulating the Population of Conformational Clusters DOI
Lipika Baidya, Hiranmay Maity, Govardhan Reddy

et al.

The Journal of Physical Chemistry B, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 20, 2025

Salts readily alter the physical properties of intrinsically disordered proteins (IDPs) rich in charged residues. Using a coarse-grained IDP model and computer simulations, we investigated how salts affect heterogeneous conformational ensemble segment-level structures prothymosin-α, classified as polyelectrolyte. We show that clusters conformations with distinct structural features are present within prothymosin-α by projecting it onto two-dimensional latent space aid autoencoders. Although is inherently disordered, there preferred transitions between these conformations. Changing salt concentration led to formation new or/and disappearance existing clusters, contributing changes properties. Shuffling Skopelitian domain (C-terminal sequence) known for its anticancer activity, resulted different cluster, indicating specific related particular function. The multiple could be correlated functions, or inhibit functions modulating population clusters.

Language: Английский

Citations

0
Deep Learning-Driven Computational Approaches for Studying Intrinsically Disordered Regions in S100-A9 DOI

Gionathan L Distefano,

Fabio D’Amico

Methods in molecular biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

0
IPAMD: A Plugin-Based Software for Biomolecular Condensate Simulations DOI
Xiaoyang Liu, You‐Liang Zhu, Yuze Jiang

et al.

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: May 27, 2025

The study of intrinsically disordered proteins (IDPs) and their role in biomolecular condensate formation has become a critical area research, offering insights into fundamental biological processes therapeutic development. Here, we present IPAMD (Intrinsically Protein Aggregation Molecular Dynamics), plugin-based software designed to simulate the dynamics condensates IDPs. provides modular, efficient, customizable simulation platform specifically for studies. It incorporates advanced force fields, such as HPS-based Mpipi models, employs optimization techniques large-scale simulations. features user-friendly interface supports batch processing, making it accessible researchers with varying computational expertise. Benchmarking case studies demonstrate ability accurately analyze structures properties.

Language: Английский

Citations

0