ConSurfDB vs. ConSurf: Difference between revisions
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In brief, the [http://consurf.tau.ac.il ConSurf Server] uses the following process by default: | In brief, the [http://consurf.tau.ac.il ConSurf Server] uses the following process by default: | ||
# Obtains the protein sequence for the specified PDB code (or uploaded PDB file) and chain. | # Obtains the protein sequence for the specified PDB code (or uploaded PDB file) and chain. | ||
# Gathers closely related sequences from | # Gathers closely related sequences from UNIREF90 (or another database that you specify) with a PSI-BLAST search. E value cutoff<ref name="evalue" />, number of iterations, and number of sequences to use are configurable. | ||
# Filters the sequences, by default eliminating those redundant at 95% or higher identity with each other, and those with less than 35% sequence identity to the query sequence. These percentages are adjustable. | # Filters the sequences, by default eliminating those redundant at 95% or higher identity with each other, and those with less than 35% sequence identity to the query sequence. These percentages are adjustable. | ||
#Optionally enables the user to manually select which sequences will be used, from a list with checkboxes. In particular, this enables users to limit the analysis to proteins having the same function as the protein of interest (see [[#Limiting ConSurf Analysis to Proteins of a Single Function|above]]). | #Optionally enables the user to manually select which sequences will be used, from a list with checkboxes. In particular, this enables users to limit the analysis to proteins having the same function as the protein of interest (see [[#Limiting ConSurf Analysis to Proteins of a Single Function|above]]). | ||
