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PDB ID Each structure in the PDB is represented by a 4 character alphanumeric identifier, assigned upon its deposition. For example, 1bxl and 1d66 are identification codes for PDB entries for Bcl-Xl / Bak complex and Gal4 (Residues 1 - 65) complex with 19mer DNA, respectively. For more information check the PDB
home page
User-Provided PDB file The PSI-BLAST
search for homologues is done using the sequence extracted from the SEQRES
record, or from the ATOM
record in case the SEQRES record is missing. The ATOM record is
essential
for ConSurf run; therefore it must be included in the user-provided PDB
file.
Chain Identifier To run ConSurf you should specify a Chain Identifier (A, B, C, in the corresponding field of the PDB file). If no chain is specified in the PDB file, please type 'none' on the chain field. One way to get the chain identifier is to display the molecule in FirstGlance in Jmol and click on the chain of interest. The chain identifier is reported in the message box at the lower left frame. You can also find the chain identifiers of a standard PDB file on the third field (column 12) of the SEQRES records or the sixth field (column 22) of the ATOM records. The chain identifier may be any single legal character, including a blank character, which is used if there is only one chain. For more information check the PDB File Format Contents Guide
E-value (PSI-BLAST) The Expectation value (E-value) is a parameter that describes the number of hits one can "expect" to see just by chance when searching a database of a particular size. It decreases exponentially with the Score (S) that is assigned to a match between two sequences. Essentially, the E-value describes the random background noise that exists for matches between sequences. The lower the E-value, the more significant the score. The Expectation value is used as a convenient way to create a significance threshold for reporting results. For example, the meaning of an E-value of 1 assigned to a hit is that in a database of the current size one might expect to see 1 match with a similar score simply by chance. Using a higher E-value will probably yield more hits, but their distance from the query sequence will increase. This field is irrelevant for a
user-provided MSA
file.
Maximum Number of Homologues The maximum number of homologues, from those found by PSI-BLAST (with the given E-value), to be included in the calculation. In order to include all the homologues, replace the default value with the word "all". This field is irrelevant for a user
provided MSA
file.
User-Provided Multiple Sequence Alignment (MSA) ConSurf accepts external MSAs in the 7
formats supported
by CLUSTAL
W.
In case you provide an external MSA file, you are required to fill the "Query sequence name in MSA file" field in the ConSurf form. This is the name of the sequence in the provided MSA file that corresponds to the query chain of the selected PDB structure. In case you provide an external MSA file in Fasta format, please use the "-" sign as the only gap symbol, as this is the only standard gap sign that ConSurf accepts.
Graphic Visualization The target protein chain is
represented as a space-filling model with the conservation grades
color-coded onto each amino acid van-der-Waals surface. All other
chains in the PDB file are displayed in backbone representation and all
ligands are presented in ball-and-stick representation. Reliability of the results Calculation qualityMinimal Requirements for a Successful ConSurf Run
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