Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
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| Title: | Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families |
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| Authors: | Parra, r. Gonzalo, Freiberger, Maria I, Poley Gil, Miriam, Fernandez Martin, Miguel, Radusky, Leandro G, Ruiz Serra, Victoria, Wolynes, Peter G, Ferreiro, Diego U, Valencia, Alfonso |
| Contributors: | Barcelona Supercomputing Center |
| Source: | Nucleic Acids Res UPCommons. Portal del coneixement obert de la UPC Universitat Politècnica de Catalunya (UPC) |
| Publisher Information: | Oxford University Press (OUP), 2024. |
| Publication Year: | 2024 |
| Subject Terms: | Models, Molecular, 0301 basic medicine, Protein Folding, Internet, 0303 health sciences, Folded proteins, Protein Conformation, Protein, Proteins, Evolution, Molecular, 03 medical and health sciences, Protein structure prediction, Simulació per ordinador, Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Web Server Issue, Thermodynamics, Software, Principle of Minimal Frustration |
| Description: | 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. |
| Document Type: | Article Other literature type |
| File Description: | application/pdf |
| Language: | English |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkae244 |
| Access URL: | https://pubmed.ncbi.nlm.nih.gov/38587198 https://hdl.handle.net/2117/413331 https://doi.org/10.1093/nar/gkae244 |
| Rights: | CC BY NC |
| Accession Number: | edsair.doi.dedup.....f3f1d8cffe2f3a6ca0d17104767a7b3a |
| Database: | OpenAIRE |
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Nájsť tento článok vo Web of Science | 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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| ISSN: | 13624962 03051048 |
| DOI: | 10.1093/nar/gkae244 |