HBonanza 1.01- Molecular-Dynamics-Trajectory Hydrogen-Bond Analysis

HBonanza 1.01

:: DESCRIPTION

HBonanza (hydrogen-bond analyzer) is a software that aids the analysis and visualization of hydrogen-bond networks. HBonanza, which can be used to analyze single structures or the many structures of a molecular dynamics simulation, is open source and python implemented, making it easily editable, customizable, and platform independent.

::DEVELOPER

Jacob Durrant, @ the lab of Rommie E. Amaro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

HBonanza

:: MORE INFORMATION

Citation

J Mol Graph Model. 2011 Nov;31:5-9. doi: 10.1016/j.jmgm.2011.07.008. Epub 2011 Aug 7.
HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis.
Durrant JD1, McCammon JA.

HBAT 1.1 – Hydrogen Bond Analysis Tool

HBAT 1.1

:: DESCRIPTION

HBAT (Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. Other related tools available from HBAT Project are PDIA(Post Docking Interaction Analysis) and HBNG(Hydrogen Bond Network Graph).

::DEVELOPER

Abhishek Tiwari & Sunil Kumar Panigrahi

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

HBAT

:: MORE INFORMATION

Citation

HBAT: a complete package for analysing strong and weak hydrogen bonds in macromolecular crystal structures.
Tiwari A, Panigrahi SK.
In Silico Biol. 2007;7(6):651-61.

H-VDW – Predicting Hydrogen Bonds or van der Waals contacts in Protein-nucleic acid Complexes

H-VDW

:: DESCRIPTION

H-VDW is a novel method for quantitatively predicting non-covalent interactions from protein and nucleic acid sequence.

::DEVELOPER

State Key Laboratory of Bioelectronics , Southeast University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Mol Graph Model. 2011 Nov;31:28-34. doi: 10.1016/j.jmgm.2011.08.001. Epub 2011 Aug 11.
A novel method for quantitatively predicting non-covalent interactions from protein and nucleic acid sequence.
Wu J, Hu D, Xu X, Ding Y, Yan S, Sun X.

HBNG 1.0 – Hydrogen Bond Network Graph

HBNG 1.0

:: DESCRIPTION

HBNG is a graph theory based tool for visualization of hydrogen bond network in 2D. Digraphs generated by HBNG facilitate visualization of cooperativity and anticooperativity chains and rings in protein structures. HBNG takes hydrogen bonds list files (output from HBAT, HBEXPLORE, HBPLUS and STRIDE) as input and generates a DOT language script and constructs digraphs using freeware AT and T Graphviz tool. HBNG is useful in the enumeration of favorable topologies of hydrogen bond networks in protein structures and determining the effect of cooperativity and anticooperativity on protein stability and folding. HBNG can be applied to protein structure comparison and in the identification of secondary structural regions in protein structures.

::DEVELOPER

Abhishek Tiwari & Sunil Kumar Panigrahi

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

HBNG

:: MORE INFORMATION