AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.

ABSTRACT:

Motivation

The full description of nucleic acid conformation involves eight torsion angles per nucleotide. To simplify this description, we previously developed a representation of the nucleic acid backbone that assigns each nucleotide a pair of pseudo-torsion angles (eta and theta defined by P and C4' atoms; or eta' and theta' defined by P and C1' atoms). A Java program, AMIGOS II, is currently available for calculating eta and theta angles for RNA and for performing motif searches based on eta and theta angles. However, AMIGOS II lacks the ability to parse DNA structures and to calculate eta' and theta' angles. It also has little visualization capacity for 3D structure, making it difficult for users to interpret the computational results.

Results

We present AMIGOS III, a P

SUBMITTER: Shine M 

PROVIDER: S-EPMC9113296 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature