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Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
Open accessPublished version of a preprint
Abstract
According to the Principle of Minimal Frustration, folded proteins can only have a minimal number of strong energetic conflicts in their native states. However, not all interactions are energetically optimized for folding but some remain in energetic conflict, i.e. they are highly frustrated. This remaining local energetic frustration has been shown to be statistically correlated with distinct functional aspects such as protein-protein interaction sites, allosterism and catalysis. Fuelled by the recent breakthroughs in efficient protein structure prediction that have made available good quality models for most proteins, we have developed a strategy to calculate local energetic frustration within large protein families and quantify its conservation over evolutionary time. Based on this evolutionary information we can identify how stability and functional constraints have appeared at the common ancestor of the family and have been maintained over the course of evolution. Here, we present FrustraEvo, a web server tool to calculate and quantify the conservation of local energetic frustration in protein families.
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Cites
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Metadata
- Authors
- Parra, R. G., Freiberger, M. I., Poley-Gil, M., Fernandez-Martin, M., Radusky, L. G., Ruiz-Serra, V., Wolynes, P. G., Ferreiro, D. U., & Valencia, A.
- Affiliations
- Barcelona Supercomputing Center (ES)
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires C1428EGA, Argentina
- Manas.tech , 300 Lenora Street 1541, Seattle, WA 98121, USA
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center , Barcelona, Spain
- Center for Theoretical Biological Physics (US)
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Corresponding author
- Parra, R Gonzalo
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-04-08
- Volume
- 52
- Issue
- W1
- Pages
- W233-W237
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC11223790
- OpenAlex
- W4394578939
- Cited by
- 10
- References
- 1
- Citations by year
- 2026: 5 · 2025: 3 · 2024: 2
- FWCI
- 1.36
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Conicet (publishedVersion, cc-by-nc)
- UPCommons institutional repository (Universitat Politècnica de Catalunya) (submittedVersion, cc-by-nc-nd)
- Rice Research Repository (Rice University) (submittedVersion, cc-by-nc)
- Funders
- Instituto de Salud Carlos III (IHMC22/00007)
- European Union NextGenerationEU/PRTR
- Consejo de Investigaciones Cientificas y Tecnicas
- CONICET (PIP2022-2024 - 11220210100704CO)
- Universidad de Buenos Aires (20020220200106BA)
- Center for Theoretical Biological Physics (PHY-2019745)
- Rice University (C-0016)
- Barcelona Supercomputing Center
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- protein families, protein folding, evolutionary conservation, protein stability, protein-protein interaction sites, catalysis, web server
- MeSH terms
- Models, Molecular, Protein Conformation, Proteins, Software, Thermodynamics, Protein Folding, Evolution, Molecular, Internet
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