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

Abhishek Tiwari

TL;DR

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 and offers improved cross-platform tkinter-based graphical user interface (GUI) and a web-based interface.

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$$π$, $π$-$π$ stacking, and n$\rightarrow$$π$* 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.

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

TL;DR

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 and offers improved cross-platform tkinter-based graphical user interface (GUI) and a web-based interface.

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, - stacking, and n* 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.
Paper Structure (25 sections, 5 figures)

This paper contains 25 sections, 5 figures.

Table of Contents

  1. Abstract
  2. Keywords
  3. Introduction
  4. Methods
  5. Implementation
  6. Structure Preparation
  7. Interaction Detection
  8. Cooperativity Analysis
  9. 3D Visualization
  10. Parameter Presets
  11. Output Formats
  12. Operation
  13. Use Cases
  14. Structure-based drug design
  15. Protein engineering
  16. ...and 10 more sections

Figures (5)

  • Figure 1: The latest update to HBAT 2 uses tkinter to provide a cross-platform graphical user interface (GUI)
  • Figure 2: HBAT 2 analysis workflow showing the complete pipeline from PDB input to multiple output formats
  • Figure 3: C-H$\cdots$$\pi$ interaction between A:ALA:20 → A:TYR:25 of PDB Structure 6RSA
  • Figure 4: HBAT 2 is also available as a web server and supports analysis of PDB files up to 1MB.
  • Figure 5: An example visualisation of potential cooperativity chain generated by HBAT 2 software for Protein Data Bank (PDB) entry 4X21