ConSurfDB vs. ConSurf: Difference between revisions
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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'''. | 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 improvement (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 need to be adjusted in order to get an optimally informative result. For an example with default settings, see the [http://consurfdb.tau.ac.il/comparison.php cytochrome c comparision at ConSurf-DB]. 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]]). | ||
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 (Swiss-Prot or UniProt), set the Expectation cutoff<ref name="evalue" />, set the number of PSI-BLAST 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 Also you can upload your own PDB file, which enables you to process unpublished data, theoretical models, or "trimmed" chains, e.g. a domain of interest from a long chain.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 (Swiss-Prot or UniProt), set the Expectation cutoff<ref name="evalue" />, set the number of PSI-BLAST 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 long chain. | ||
