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- PANAV abstract "PANAV (Probabilistic Approach for protein NMR Assignment Validation) is a freely available stand-alone program that is used for protein chemical shift re-referencing [1]. Chemical shift referencing is a problem in protein NMR as >20% of reported NMR chemical shift assignments appear to be improperly referenced [1]. For certain nuclei (especially 13C and 15N) these referencing issues can cause systematic chemical shift errors of between 1.0 to 2.5 ppm. Chemical shift errors of this magnitue often make it very difficult to compare NMR chemical shift assignments between proteins. It also makes it very hard to structurally interpret chemical shifts (i.e. identify secondary structures or perform chemical shift refinement). Unlike most other chemical shift re-referencing tools [2,3] PANAV employs a structure-independent protocol [1]. That is, with PANAV there is no need to know the structure of the protein in advance of correcting any chemical shift referencing errors. This makes PANAV particularly useful for NMR studies involving novel or newly assigned proteins, where the structure has yet to be determined. Indeed, this scenario represents the vast majority of assignment cases in biomolecular NMR. PANAV uses residue-specific and secondary structure-specific chemical shift distributions that were calculated over short (3-6 residue) fragments of correctly referenced proteins (found in RefDB [2]) to identify mis-assigned resonances. More specifically, PANAV compares the initial (i.e. observed) chemical shift assignments to the expected chemical shifts based on their local sequence and expected/predicted secondary structure. In this way, PANAV is able to identify and re-reference mis-referenced chemical shift assignments. PANAV can also identify potentially mis-assigned resonances as well. PANAV has been extensively tested and compared against a large number of existing re-referencing or mis-assignment detection programs (most of which are structure-based). These assessments indicate that PANAV is equal to or superior to existing approaches. PANAV is available at http://www.wishartlab.com/web_servers/panav".
- PANAV title "PANAV".
- PANAV wikiPageExternalLink panav.
- PANAV wikiPageID "42516350".
- PANAV wikiPageRevisionID "605941085".
- PANAV center "University of Alberta".
- PANAV curation "Manually curated".
- PANAV description "For protein chemical shift re-referencing".
- PANAV laboratory "Dr. David Wishart".
- PANAV scope "Data input: Chemical shift assignments in BMRB or SHIFTY format ; Data output: Reference-corrected chemical shift assignments".
- PANAV title "PANAV".
- PANAV url panav.
- PANAV description "For protein chemical shift re-referencing".
- PANAV type BiologicalDatabase.
- PANAV type Database.
- PANAV type Work.
- PANAV type CreativeWork.
- PANAV type InformationEntity.
- PANAV type InformationObject.
- PANAV comment "PANAV (Probabilistic Approach for protein NMR Assignment Validation) is a freely available stand-alone program that is used for protein chemical shift re-referencing [1]. Chemical shift referencing is a problem in protein NMR as >20% of reported NMR chemical shift assignments appear to be improperly referenced [1]. For certain nuclei (especially 13C and 15N) these referencing issues can cause systematic chemical shift errors of between 1.0 to 2.5 ppm.".
- PANAV label "PANAV".
- PANAV sameAs m.010f7rps.
- PANAV sameAs Q17142923.
- PANAV sameAs Q17142923.
- PANAV wasDerivedFrom PANAV?oldid=605941085.
- PANAV homepage panav.
- PANAV isPrimaryTopicOf PANAV.