Dataset Information

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 PyMOL plugin that calculates the pseudo-torsion angles eta, theta, eta' and theta' for both DNA and RNA structures and performs motif searching based on these angles. Compared to AMIGOS II, AMIGOS III offers improved pseudo-torsion angle visualization for RNA and faster nucleic acid worm database generation; it also introduces pseudo-torsion angle visualization for DNA and nucleic acid worm visualization. Its integration into PyMOL enables easy preparation of tertiary structure inputs and intuitive visualization of involved structures.

Availability and implementation

https://github.com/pylelab/AMIGOSIII.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Shine M

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

REPOSITORIES: biostudies-literature

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Publications

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

Shine Morgan M Zhang Chengxin C Pyle Anna Marie AM

Bioinformatics (Oxford, England) 20220501 10

<h4>Motivation</h4>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 base ...[more]

PMID: 35561202

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Project description:This groundbreaking study derives and tests several new dihedral torsion model potentials for constructing classical forcefields for atomistic simulations of materials. (1) The new angle-damped dihedral torsion (ADDT) model potential is preferred when neither contained equilibrium bond angle is linear (i.e., (θ eq ABC and θ eq BCD) ≠ 180°), at least one of the contained equilibrium bond angles is ≥ 130° (i.e., (θ eq ABC or θ eq BCD) ≥ 130°), and the dihedral torsion potential contains some odd-function contributions (i.e., U[ϕ] ≠ U[-ϕ]). (2) The new angle-damped cosine only (ADCO) model potential is preferred when neither contained equilibrium bond angle is linear (i.e., (θ eq ABC and θ eq BCD) ≠180°), at least one of the contained equilibrium bond angles is ≥ 130° (i.e., (θ eq ABC or θ eq BCD) ≥ 130°), and the dihedral torsion potential contains no odd-function contributions (i.e., U[ϕ] = U[-ϕ]). (3) The new constant amplitude dihedral torsion (CADT) model potential is preferred when neither contained equilibrium bond angle is linear (i.e., (θ eq ABC and θ eq BCD) ≠ 180°), both contained equilibrium bond angles are <130° (i.e., (θ eq ABC and θ eq BCD) < 130°), and the dihedral torsion potential contains some odd-function contributions (i.e., U[ϕ] ≠ U[-ϕ]). (4) The constant amplitude cosine only (CACO) model potential is preferred when neither contained equilibrium bond angle is linear (i.e., (θ eq ABC and θ eq BCD) ≠180°), both contained equilibrium bond angles are <130° (i.e., (θ eq ABC and θ eq BCD) <130°), and the dihedral torsion potential contains no odd-function contributions (i.e., U[ϕ] = U[-ϕ]). (5) The new angle-damped linear dihedral (ADLD) model potential is preferred when at least one contained equilibrium bond angle is linear (i.e., (θ eq ABC or θ eq BCD) = 180°). Most importantly, this article derives combined angle-dihedral coordinate branch equivalency conditions and angle-damping factors that ensure the angle-damped torsion model potentials (e.g., ADDT, ADCO, and ADLD) are mathematically consistent and continuously differentiable even as at least one contained bond angle approaches linearity (i.e., as (θ ABC or θ BCD) → 180°). This article introduces the torsion offset potential (TOP). I show the TOP gives rise in some materials to the unusual physical phenomenon of slip torsion. For various molecules, extensive quantitative comparisons to high-level quantum chemistry calculations (e.g., CCSD) and experimental vibrational frequencies showed these new dihedral torsion model potentials perform superbly.

Dataset Information

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

Motivation

Results

Availability and implementation

Supplementary information

Publications

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

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