A curated rotamer library for common post-translational modifications of proteins.
Bioinformatics
; 40(7)2024 07 01.
Article
in En
| MEDLINE
| ID: mdl-38995731
ABSTRACT
MOTIVATION Sidechain rotamer libraries of the common amino acids of a protein are useful for folded protein structure determination and for generating ensembles of intrinsically disordered proteins (IDPs). However, much of protein function is modulated beyond the translated sequence through the introduction of post-translational modifications (PTMs). RESULTS:
In this work, we have provided a curated set of side chain rotamers for the most common PTMs derived from the RCSB PDB database, including phosphorylated, methylated, and acetylated sidechains. Our rotamer libraries improve upon existing methods such as SIDEpro, Rosetta, and AlphaFold3 in predicting the experimental structures for PTMs in folded proteins. In addition, we showcase our PTM libraries in full use by generating ensembles with the Monte Carlo Side Chain Entropy (MCSCE) for folded proteins, and combining MCSCE with the Local Disordered Region Sampling algorithms within IDPConformerGenerator for proteins with intrinsically disordered regions. AVAILABILITY AND IMPLEMENTATION The codes for dihedral angle computations and library creation are available at https//github.com/THGLab/ptm_sc.git.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Proteins
/
Protein Processing, Post-Translational
/
Databases, Protein
/
Intrinsically Disordered Proteins
Language:
En
Journal:
Bioinformatics
/
Bioinformatics (Oxford. Online)
Journal subject:
INFORMATICA MEDICA
Year:
2024
Document type:
Article
Affiliation country:
Estados Unidos
Country of publication:
Reino Unido