11 lines
755 B
Text
11 lines
755 B
Text
Given a GCG multiple sequence alignment file (a GCG MSF file), which a
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includes a sequence of known structure, the program pdbalign maps the
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sequence variability onto the known structure. The central premise is
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of course, that for a closely related family of proteins (sequence ID
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> 40%) the 3-D structures will not be significantly different.pdbdist
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calculates the distance from each atom in the pdb file to each atom in
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the ligand and records the minimum in the temperature field for that
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atom record.distalign reads the output from pdbdist and also the
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original GCG MSF file and produces an MSF file annotated with a
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measure of sequence variability and the distance of the residue at
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that position (of the sequence of known structure) from the ligand.
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