UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations.

IF 4.7 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology Pub Date : 2025-01-31 DOI:10.1016/j.jmb.2025.168968

Rafał Ślusarz, Adam K Sieradzan, Artur Giełdoń, Emilia A Lubecka, Magdalena J Ślusarz, Mateusz Leśniewski, Nguyen Truong Co, Adam Liwo, Cezary Czaplewski

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引用次数: 0

Abstract

The third version of the UNRES web server is described, in which the range of biological macromolecules treated and calculation types has been extended significantly. DNA and RNA molecules have been added to enable the user to run simulations of their folding/hybridization and dynamics. To increase the accuracy of the simulated proteins models, the restraints on secondary structure have been enhanced to include the probabilities of the coil, extended and helical state, which are taken from the PSIPRED or HHpred raw input and the restraints from multiple bioinformatics models have been added. The NMR-data-assisted functionality has been extended to include time-averaged restraints, this feature enabling the user to model multistate and intrinsically-disordered proteins and those with intrinsically-disordered regions. Finally, the prediction of the propensity of peptides to aggregation has been included to enable the user to predict peptide solubility and aggregation, including the character and the structures of the aggregates.

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来源期刊

Journal of Molecular Biology 生物-生化与分子生物学

CiteScore

11.30

自引率

1.80%

发文量

412

审稿时长

28 days

期刊介绍： Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.