Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics
The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins' biological behavior. It compares the energy distributions of the na...
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13624962_v44_nW1_pW356_Parra http://hdl.handle.net/20.500.12110/paper_13624962_v44_nW1_pW356_Parra |
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paper:paper_13624962_v44_nW1_pW356_Parra2023-06-08T16:11:37Z Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics Ferreiro, Diego U. nuclear protein nucleic acid nucleosome algorithm amino acid sequence chemistry computer graphics computer interface genetics human Internet molecular dynamics nucleosome protein domain protein folding protein secondary structure sequence analysis static electricity thermodynamics Algorithms Amino Acid Sequence Computer Graphics Humans Internet Molecular Dynamics Simulation Nuclear Proteins Nucleic Acids Nucleosomes Protein Folding Protein Interaction Domains and Motifs Protein Structure, Secondary Sequence Analysis, Protein Static Electricity Thermodynamics User-Computer Interface The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins' biological behavior. It compares the energy distributions of the native state with respect to structural decoys. The network of minimally frustrated interactions encompasses the folding core of the molecule. Sites of high local frustration often correlate with functional regions such as binding sites and regions involved in allosteric transitions. We present here an upgraded version of a webserver that measures local frustration. The new implementation that allows the inclusion of electrostatic energy terms, important to the interactions with nucleic acids, is significantly faster than the previous version enabling the analysis of large macromolecular complexes within a user-friendly interface. The webserver is freely available at URL: http://frustratometer.qb.fcen.uba.ar. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. Fil:Ferreiro, D.U. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2016 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13624962_v44_nW1_pW356_Parra http://hdl.handle.net/20.500.12110/paper_13624962_v44_nW1_pW356_Parra |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
nuclear protein nucleic acid nucleosome algorithm amino acid sequence chemistry computer graphics computer interface genetics human Internet molecular dynamics nucleosome protein domain protein folding protein secondary structure sequence analysis static electricity thermodynamics Algorithms Amino Acid Sequence Computer Graphics Humans Internet Molecular Dynamics Simulation Nuclear Proteins Nucleic Acids Nucleosomes Protein Folding Protein Interaction Domains and Motifs Protein Structure, Secondary Sequence Analysis, Protein Static Electricity Thermodynamics User-Computer Interface |
| spellingShingle |
nuclear protein nucleic acid nucleosome algorithm amino acid sequence chemistry computer graphics computer interface genetics human Internet molecular dynamics nucleosome protein domain protein folding protein secondary structure sequence analysis static electricity thermodynamics Algorithms Amino Acid Sequence Computer Graphics Humans Internet Molecular Dynamics Simulation Nuclear Proteins Nucleic Acids Nucleosomes Protein Folding Protein Interaction Domains and Motifs Protein Structure, Secondary Sequence Analysis, Protein Static Electricity Thermodynamics User-Computer Interface Ferreiro, Diego U. Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics |
| topic_facet |
nuclear protein nucleic acid nucleosome algorithm amino acid sequence chemistry computer graphics computer interface genetics human Internet molecular dynamics nucleosome protein domain protein folding protein secondary structure sequence analysis static electricity thermodynamics Algorithms Amino Acid Sequence Computer Graphics Humans Internet Molecular Dynamics Simulation Nuclear Proteins Nucleic Acids Nucleosomes Protein Folding Protein Interaction Domains and Motifs Protein Structure, Secondary Sequence Analysis, Protein Static Electricity Thermodynamics User-Computer Interface |
| description |
The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins' biological behavior. It compares the energy distributions of the native state with respect to structural decoys. The network of minimally frustrated interactions encompasses the folding core of the molecule. Sites of high local frustration often correlate with functional regions such as binding sites and regions involved in allosteric transitions. We present here an upgraded version of a webserver that measures local frustration. The new implementation that allows the inclusion of electrostatic energy terms, important to the interactions with nucleic acids, is significantly faster than the previous version enabling the analysis of large macromolecular complexes within a user-friendly interface. The webserver is freely available at URL: http://frustratometer.qb.fcen.uba.ar. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| author |
Ferreiro, Diego U. |
| author_facet |
Ferreiro, Diego U. |
| author_sort |
Ferreiro, Diego U. |
| title |
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics |
| title_short |
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics |
| title_full |
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics |
| title_fullStr |
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics |
| title_full_unstemmed |
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics |
| title_sort |
protein frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics |
| publishDate |
2016 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13624962_v44_nW1_pW356_Parra http://hdl.handle.net/20.500.12110/paper_13624962_v44_nW1_pW356_Parra |
| work_keys_str_mv |
AT ferreirodiegou proteinfrustratometer2atooltolocalizeenergeticfrustrationinproteinmoleculesnowwithelectrostatics |
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1768543718070026240 |