1. Introduction

The ProBuilder service builds a 3D peptide starting from its aminoacid sequence in raw or FASTA format. It applies the secondary structure specified by the user changing the backbone torsion angles (Phi, Psi and Omega). The peptide building, the hydrogens and the amino acid side chain adding is provided by VEGA.

2. How it works

The molecule sent by the user is read by VEGA that provides the following steps:

1. construction of the protein backbone;
2. secondary structure change, applying the template specified by the user (alpha helix, left handed helix, 3.10 helix, p helix, beta strand, anti-parallel beta strand, parallel beta strand) or the Phi, Psi and Omega  torsion values;
3. adding of amino acid side chains (optional);
4. adding of hydrogens (optional);
5. conversion of the resulting structure in the user-selected file format.

No structure optimization is performed and so a MM minimization of the output structure is required.