Online server for Packing Entropy analysis using PACKMAN

Information & Instructions

This webpage will provide an interface for Packing Entropy online. Please refer to the following research article to know more about the parameters and citation:

Pranav M. Khade and Robert L. Jernigan. Entropies Derived from the Packing Geometries within a Single Protein Structure. ACS Omega 2022 7 (24), 20719-20730 DOI: 10.1021/acsomega.2c00999

For more information on the PACKMAN visit https://github.com/Pranavkhade/PACKMAN

Entropy Type

Provide the Entropy type (Options: 1. PackingEntropy)

CIF/PDB file

NOTE: Please check if the input file contains any hydrogen atoms as it might get considered as heavy atoms in some cases.

PDB ID

If provided, the PBD with this ID will be downloaded and used as the input file.

Chains to be used for the entropy calculation

Recommended: None. Chain IDs for the Entropy calculation (None means all the chains are included; single string means only one chain ID; multiple chains should be comma separated).'

Size surface probe radius

Recommended: 1.4 (radius of a water molecule), Please refer to the paper for more details

Number of points on a sphere

Recommended: 30. Number of points to be generated around each point for the surface (Read the Publication for more details)

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