Dataset Information

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.

SUBMITTER: Parra RG

PROVIDER: S-EPMC4987889 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics.

Parra R Gonzalo RG Schafer Nicholas P NP Radusky Leandro G LG Tsai Min-Yeh MY Guzovsky A Brenda AB Wolynes Peter G PG Ferreiro Diego U DU

Nucleic acids research 20160429 W1

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 ...[more]

PMID: 27131359

Similar Datasets

Project description:Introduction: Psychometric tools have been developed for the assessment of behavioral and affective traits in non-human animals. Frustration can be defined as an emotional reaction experienced after a given expectation is violated. Frustration is a negative emotional state and whilst it probably plays a key role in certain behavior problems in dogs (e.g., aggressive behaviors), there appears to have been little attempt to scale this affective tendency. Therefore, the aim of the current study was to develop a tool to assess frustration tendencies in dogs. Materials and Methods: An online owner survey was developed. Items covered demographics, the training/behavioral history of the dog, and 33 frustration related items scored using a 5-point Likert scale. The questionnaire was disseminated via on-line channels over a 5-month period. Two thousand three hundred forty-eight respondents completed the questionnaire. Of these, 273 respondents completed it a second time 6 weeks later, and a separate 276 respondents completed it a second time 1 year later. Additionally, 92 paired responses were collected where two carers completed the questionnaire independently about the same dog. Intra- and inter-rater reliabilities were assessed prior to structuring the items using principal component analysis (PCA) with a Varimax rotation. Items were retained if they loaded > 0.4 on at least one of the components extracted using the Kaiser criterion. Results: Twenty-two items were deemed to be reliable enough to be used in the PCA and 21 items loaded on a biologically meaningful 5-principal component solution. There was a significant positive correlation between each principal component and the owners' general perception of their dogs' frustration tendencies, alongside other expected correlates. Conclusion: This is the first reliable psychometric tool for the assessment of frustration in dogs-the Canine Frustration Questionnaire (CFQ). Further validation with behavioral tests and physiological measures is ongoing.

Dataset Information

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics.

Publications

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets