ConSurfDB vs. ConSurf: Difference between revisions
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When the [[Interpreting ConSurf Results|Average Pairwise Distance]] (APD) in the multiple sequence alignment (MSA) approaches or exceeds approximately 1.0, it is likely that proteins with multiple functions have been included in the MSA. To see conservation that reflects the function of the query protein, it is best to use an MSA with an APD in roughly the range 0.3-0.6. Sometimes, the ConSurf Server's result with default settings may give such a result. If not, you may wish to do additional ConSurf runs with the goal of reducing the APD. | When the [[Interpreting ConSurf Results|Average Pairwise Distance]] (APD) in the multiple sequence alignment (MSA) approaches or exceeds approximately 1.0, it is likely that proteins with multiple functions have been included in the MSA. To see conservation that reflects the function of the query protein, it is best to use an MSA with an APD in roughly the range 0.3-0.6. Sometimes, the ConSurf Server's result with default settings may give such a result. If not, you may wish to do additional ConSurf runs with the goal of reducing the APD. | ||
Prior to 2022, the ConSurf Server enabled manual selection of sequences. Unfortunately, after a 2022 update to the ConSurf Server, this is no longer practical. Hence we are limited to adjusting run parameters by trial and error "in the dark". | Prior to 2022, the ConSurf Server enabled manual selection of sequences. Unfortunately, after a 2022 update to the ConSurf Server, this is no longer practical. Hence we are limited to adjusting run parameters by trial and error "in the dark" until satisfactory results are obtained. | ||
#Go to [http://consurf.tau.ac.il consurf.tau.ac.il], the ConSurf Server (distinct from ConSurf-DB). | #Go to [http://consurf.tau.ac.il consurf.tau.ac.il], the ConSurf Server (distinct from ConSurf-DB). | ||
