NIAS-Server

NIAS-Server
Neighbors Influence of Amino Acids and Secondary Structures
Updated by January 2021
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Target Amino Acid Sequence

Secondary Structure

For secondary structure prediction use PsiPred

APLs


Database






What is NIAS?

NIAS is a server to analyze the conformational preferences of amino acid residues in proteins.

Background

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.

Instructions

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: mdorn@inf.ufrgs.br

Citing NIAS

If you use NIAS in a scientific publication, we would appreciate citations to the following paper:

Publications

There are some papers already using NIAS! These are some: