MutationExplorer : a webserver for mutation of proteins and 3D visualization of energetic impacts
Open accessPublished version of a preprint
Abstract
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/.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
ClinVar: improving access to variant interpretations and supporting evidence
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<scp>ESM</scp> ‐scan—A tool to guide amino acid substitutions
Totaro, M. G., Vide, U., Zausinger, R., Winkler, A., & Oberdorfer, G. (2024) · Protein Science · doi:10.1002/pro.5221 · Cited by 19 · see citing works
- Authors
- Philipp, M., Moth, C. W., Ristic, N., Tiemann, J. K. S., Seufert, F., Panfilova, A., Meiler, J., Hildebrand, P. W., Stein, A., Wiegreffe, D., & Staritzbichler, R.
- Affiliations
- Leipzig University (DE)
- Vanderbilt University (US)
- Novozymes (Denmark) (DK)
- University of Copenhagen (DK)
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE)
- Bielefeld University (DE)
- Corresponding author
- Wiegreffe, Daniel
- Staritzbichler, René
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-04-22
- Volume
- 52
- Issue
- W1
- Pages
- W132-W139
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC11223880
- OpenAlex
- W4395010845
- Cited by
- 35
- References
- 4
- Citations by year
- 2026: 12 · 2025: 18 · 2024: 4 · 2023: 1
- FWCI
- 4.61
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by-nc)
- Funders
- Deutsche Forschungsgemeinschaft (421152132)
- Federal Ministry of Education and Research of Germany
- Sächsische Staatsministerium für Wissenschaft, Kultur und Tourismus
- Protein Interactions and Stability in Medicine and Genomics
- Novo Nordisk Foundation (NNF18OC0033950)
- Lundbeck Foundation (R272-2017-4528)
- DFG (421152132, 209933838, 460865652)
- Alexander von Humboldt Foundation
- DAAD
- NIH (R01 HL122010, R01 DA046138, R01 AG068623, R01 CA227833, R01 LM013434, S10 OD016216, S10 OD020154, S10 OD032234, U01 AI150739)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- protein mutations, web server, sequence-structure mapping, energy change, single nucleotide polymorphisms, VCF, protein stability, protein function, Rosetta, hydrophobicity, sequence conservation
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