TopModel

A python script to quickly inspect and highlight issues in structure models.

Installation

pip install protein-topmodel

Or alternatively from GitHUB:

pip install git+https://github.com/liedllab/topmodel.git

Test Installation

topmodel --help

Command-Line Interface (CLI)

topmodel path/to/file*.pdb

TopModel is a command line tool that checks the chiralities, the amide bonds and overall VDW clashes in a structure model. Optionally, the structure can be opened in PyMOL to visualize the issues found. For this PyMOL needs to be in PATH.

Chirality

TopModel can assign L and D to aminoacids. In the command-line interface (CLI) only the D aminoacids are shown. The chirality is computed by computing a normal vector $\vec{n}$ to the plane defined by the triangle of the three highest priority atoms $A$ around the chiral center where the suffix denotes the priority.

$$\vec{n} = \overrightarrow{A_3A_1} \times \overrightarrow{A_3A_2}$$

The direction of the normal vector is determined by the orientation of the side chains. By calculating the dot product of the normal vector and a vector from the chiral center to the plane the relative orientation of the three atoms around the chiral center, and thus the chirality, can be determined from the sign of the result.

$$ chirality = \vec{n} \cdot \overrightarrow{A_3A_{center}} = \begin{cases} \mathbf{D}, \text{if } > 0 \\ \mathbf{L}, \text{if } < 0 \end{cases} $$

Amide bonds

TopModel can assign CIS and TRANS to the amide bonds depending on the dihedral angle defined by $C_{\alpha}CNC_\alpha$. Amide bonds that could not be assigned to either CIS or TRANS are labeled as NON_PLANAR.

Cis amide bonds to prolines are labelled separately as they occur more frequently.

Clashes

TopModel detects Van der Waals clashes by calculating the distance between all pair of atoms that are within 5 Å of each other. A clash is defined by: $$d_{AB} &lt; r_A + r_B - 0.5Å$$

As a package

TopModel can be imported as a package. The package contains the small modules chirality, amide_bond and clashes that provide functions to calculate the respective property.

import topmodel # or
from topmodel.check import chirality, amide_bond, clashes

Dependencies

• biopython
• scipy
• mendeleev
• Click
• colorama
• PyMOL (to open the structure in PyMOL)