ConSurfDB vs. ConSurf: Difference between revisions
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:{{Yelspan| In January 2018: ConSurfDB had not been updated with new entries in the [[Protein Data Bank]] since January, 2013. }} | :{{Yelspan| In January 2018: ConSurfDB had not been updated with new entries in the [[Protein Data Bank]] since January, 2013. }} | ||
Because results from the ConSurf DataBase server, [http://consurfdb.tau.ac.il ConSurf-DB]<ref name="consurfdb">PMID: 18971256</ref> are displayed within Proteopedia as ''Evolutionary Conservation'', an overview of its methods is provided here. ConSurf-DB pre-calculates conservation levels for each amino acid in every protein chain in the [[Protein Data Bank]]. It went into service in 2008. It uses state-of-the-art methods, all published in peer-reviewed journals<ref name="consurfdb" />. | Because results from the ConSurf DataBase server, [http://consurfdb.tau.ac.il ConSurf-DB]<ref name="consurfdb">PMID: 18971256</ref> are displayed within Proteopedia as ''Evolutionary Conservation'', an overview of its methods is provided here. ConSurf-DB '''pre-calculates''' conservation levels for each amino acid in every protein chain in the [[Protein Data Bank]]. It went into service in 2008. It uses state-of-the-art methods, all published in peer-reviewed journals<ref name="consurfdb" />. | ||
===ConSurf-DB Process=== | ===ConSurf-DB Process=== | ||
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==The ConSurf Server== | ==The ConSurf Server== | ||
The [http://consurf.tau.ac.il ConSurf Server], first available in 2001<ref>PMID: 11243830</ref><ref>PMID: 12499312</ref><ref>PMID: 15980475</ref> with many subsequent enhancements, can calculate and display the conservation pattern for 3D structures '''completely automatically'''. It should be used whenever the pre-calculated result at the [[#The ConSurf-DB Mechanism|ConSurf-DB]] needs | The [http://consurf.tau.ac.il ConSurf Server], first available in 2001<ref>PMID: 11243830</ref><ref>PMID: 12499312</ref><ref>PMID: 15980475</ref> with many subsequent enhancements, can calculate and display the conservation pattern for 3D structures '''completely automatically'''. It should be used whenever the pre-calculated result at the [[#The ConSurf-DB Mechanism|ConSurf-DB]] is unavailable, or does not meet your needs (for example, see [[#Limiting ConSurf Analysis to Proteins of a Single Function|above]]), or if you have your own multiple sequence alignment (MSA) that you wish to use. The default settings of ConSurf may need to be adjusted in order to get an optimally informative result. The main adjustment needed is to gather an adequate number of sequences for proteins of the same function as your protein of interest (see [[#Limiting ConSurf Analysis to Proteins of a Single Function|above]]). | ||
[[ConSurf Quick Analysis Procedure|ConSurf Server job submission instructions]]. | |||
Like ConSurf-DB, the ConSurf Server uses the same state-of-the-art methods, all of which are published in peer-reviewed journal articles. Unlike ConSurf-DB's pre-calculated results the ConSurf Server permits considerable customization. For example, the user may specify the number of sequences to use, choose the database from which sequences are obtained, set the Expectation cutoff<ref name="evalue" />, set the number of HMMER iterations, or submit their own multiple sequence alignment, or phylogenetic tree. Also you can upload your own PDB file, which enables you to process unpublished data, theoretical models, or "trimmed" chains, e.g. a [[domain]] of interest from a multiple-domain chain. | Like ConSurf-DB, the ConSurf Server uses the same state-of-the-art methods, all of which are published in peer-reviewed journal articles. Unlike ConSurf-DB's pre-calculated results the ConSurf Server permits considerable customization. For example, the user may specify the number of sequences to use, choose the database from which sequences are obtained, set the Expectation cutoff<ref name="evalue" />, set the number of HMMER iterations, or submit their own multiple sequence alignment, or phylogenetic tree. Also you can upload your own PDB file, which enables you to process unpublished data, theoretical models, or "trimmed" chains, e.g. a [[domain]] of interest from a multiple-domain chain. | ||
