PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues.

ABSTRACT:

Background

In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated version of PEPstr, developed specifically for predicting the structure of peptides containing natural and non-natural/modified residues.

Results

PEPstrMOD integrates Forcefield_NCAA and Forcefield_PTM force field libraries to handle 147 non-natural residues and 32 types of post-translational modifications respectively by performing molecular dynamics using AMBER. AMBER was also used to handle other modifications like peptide cyclization, use of D-amino acids and capping of terminal residues. In addition, GROMACS was used to implement 210 non-natural side-cha

SUBMITTER: Singh S 

PROVIDER: S-EPMC4687368 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature