MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts.

Autor:	Philipp M; Image and Signal Processing Group, Department of Computer Science, Leipzig University, Augustusplatz 10, 04109 Leipzig, Germany., Moth CW; Vanderbilt University, Center for Structural Biology, 465 21st Ave South, Nashville, TN 37232, USA., Ristic N; Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany., Tiemann JKS; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N., Denmark.; Novozymes A/S, 2800 Kgs. Lyngby, Denmark., Seufert F; Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany., Panfilova A; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N., Denmark., Meiler J; Vanderbilt University, Center for Structural Biology, 465 21st Ave South, Nashville, TN 37232, USA.; Leipzig University Medical School, Institute for Drug Discovery, Brüderstraße 34, 04103 Leipzig, Germany., Hildebrand PW; Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.; Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University, Germany.; Berlin Institute of Health, 10178 Berlin, Germany., Stein A; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N., Denmark., Wiegreffe D; Image and Signal Processing Group, Department of Computer Science, Leipzig University, Augustusplatz 10, 04109 Leipzig, Germany., Staritzbichler R; Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.; University Institute for Laboratory Medicine, Microbiology and Clinical Pathobiochemistry, University Hospital of Bielefeld University, Germany.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W132-W139.
DOI:	10.1093/nar/gkae301
Abstrakt:	The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MutationExplorer webserver maps sequence changes onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D model evolves, and estimated changes in energy are highlighted. In addition to a basic per-residue input format, MutationExplorer can also upload an entire replacement sequence. Previously the purview of desktop applications, such an upload can back-mutate PDB structures to wildtype sequence in a single step. Another supported variation source is human single nucelotide polymorphisms (SNPs), genomic coordinates input in VCF format. Structures are flexibly colorable, not only by energetic differences, but also by hydrophobicity, sequence conservation, or other biochemical profiling. Coloring by interface score reveals mutation impacts on binding surfaces. MutationExplorer strives for efficiency in user experience. For example, we have prepared 45 000 PDB depositions for instant retrieval and initial display. All modeling steps are performed by Rosetta. Visualizations leverage MDsrv/Mol*. MutationExplorer is available at: http://proteinformatics.org/mutation_explorer/. (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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