title: Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics.
abstract: 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.
authors.affiliation: Protein Physiology Lab, Dep de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina.
authors.forename: R Gonzalo
authors.initials: RG
authors.lastname: Parra
authors.affiliation: Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark.
authors.forename: Nicholas P
authors.identifier: 0000-0001-9789-2516
authors.initials: NP
authors.lastname: Schafer
authors.affiliation: Structural Bioinformatics Group, Dep de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina.
authors.forename: Leandro G
authors.initials: LG
authors.lastname: Radusky
authors.affiliation: Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX 77005, USA.
authors.forename: Min-Yeh
authors.initials: MY
authors.lastname: Tsai
authors.affiliation: Protein Physiology Lab, Dep de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina.
authors.forename: A Brenda
authors.initials: AB
authors.lastname: Guzovsky
authors.affiliation: Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX 77005, USA.
authors.forename: Peter G
authors.initials: PG
authors.lastname: Wolynes
authors.affiliation: Protein Physiology Lab, Dep de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina ferreiro@qb.fcen.uba.ar.
authors.forename: Diego U
authors.initials: DU
authors.lastname: Ferreiro
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003196:Computer Graphics; D006801:Humans; D020407:Internet; D056004:Molecular Dynamics Simulation; D009687:Nuclear Proteins / Q000737:chemistry* / Q000235:genetics; D009696:Nucleic Acids / Q000737:chemistry* / Q000235:genetics; D009707:Nucleosomes / Q000737:chemistry* / Q000235:genetics; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein; D055672:Static Electricity; D013816:Thermodynamics; D014584:User-Computer Interface
chemical_list: D009687:Nuclear Proteins; D009696:Nucleic Acids; D009707:Nucleosomes