作者
Sandeep Singh, Harinder Singh, Abhishek Tuknait, Kumardeep Chaudhary, Balvinder Singh, S Kumaran, Gajendra PS Raghava
发表日期
2015/12
期刊
Biology direct
卷号
10
期号
1
页码范围
1-19
出版商
BioMed Central
简介
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-chains in peptides using SwissSideChain force field library. We …
学术搜索中的文章
S Singh, H Singh, A Tuknait, K Chaudhary, B Singh… - Biology direct, 2015