NIAS is a server to analyze the conformational preferences
of amino acid residues in proteins.
The Angle Probability List (APL) represents the normalized
frequency of observed pairs of amino acid residues and
secondary structure in the Protein Data Bank. It combines
the conformational preferences of amino acid residues
(aa, torsion angles) in proteins with their secondary
structure information (ss).
An Angle Probability List (APL) is built from a matrix Haa,
ss of [−180, 180] × [−180, 180] cells for each amino acid
residue (aa) and secondary structure (ss). Each cell (i,j)
has the number of times that a given amino acid residue aa
in secondary structure ss has a pair of torsion angles, and
for each pair, amino acid residue and secondary structure.
An APLaa, ss represents the normalized frequency of each
pair. A higher frequency associated with a pair phi and psi
indicates that this combination is more common in nature.
The following Ramachandran maps show the conformational
profile of Glycine residue when in coil state (APL1)
according to the five structure databases considered by
NIAS is a server to help the analysis of the
conformational preferences of amino acid
residues in proteins or fragments.
How to use NIAS-server:
If you have any questions, please contact us:
If you use NIAS in a scientific publication, we would appreciate
citations to the following paper:
There are some papers already using NIAS! These are some: