HBAT 2: A Python Package to Analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures

TL;DR

HBAT 2 is a Python software package that automates the detection and analysis of hydrogen bonds and other non-covalent interactions in macromolecular structures, aiding research in structural biology and drug design.

Contribution

It introduces HBAT 2, an updated, user-friendly Python tool with enhanced interfaces and capabilities for analyzing various non-covalent interactions in PDB structures.

Findings

Supports analysis of multiple non-covalent interactions

Includes improved GUI, web, CLI, and API interfaces

Facilitates visualization and detection of interaction chains

Abstract

Hydrogen bonds and other non-covalent interactions play a crucial role in maintaining the structural integrity and functionality of biological macromolecules such as proteins and nucleic acids. Accurate identification and analysis of these interactions are essential for understanding molecular recognition, protein folding, and drug design. HBAT (Hydrogen Bond Analysis Tool) is software for analysing hydrogen bonds and other weak interactions in macromolecular structures. This paper presents HBAT 2, an updated Python reimplementation of the original HBAT tool published in 2007. HBAT 2 is a Python package for automated analysis of hydrogen bonds and other non-covalent interactions in macromolecular structures available in Protein Data Bank (PDB) file format. The software identifies and analyses traditional hydrogen bonds, weak hydrogen bonds, halogen bonds, X-H$\cdots$$\pi$, $\pi$-$\pi$ stacking, and n$\rightarrow$$\pi$* interactions using geometric criteria. It also detects cooperativity and anticooperativity chains and renders them as 2D visualisations. The latest version offers improved cross-platform tkinter-based graphical user interface (GUI), a web-based interface, a simple command-line interface (CLI), and a developer-friendly API, making it accessible to users with different computational backgrounds.