Title

AUTOMINv1.0: an automation for minimization of Protein Data Bank files and its usage

Authors

Rifat Nawaz Ul Islam^$,1, Debanjan Mitra^$,2, Parth Sarthi Sen Gupta^$,3, Sahini Banerjee^$,4,
Buddhadev Mondal^$,5, Amal Kumar Bandyopadhyay^2,*

Affiliation

¹Department of Zoology, The University of Burdwan, East Burdwan, West Bengal, India; ²Department of Biotechnology, The University of Burdwan, East Burdwan, West Bengal, India; ³Department of Chemistry, IISER Berhampur, Ganjam, Odisha, India; ⁴Department of Biological Sciences, ISI, Kolkata, West Bengal, India; 5Department of Zoology, Burdwan Raj College, East Burdwan, West Bengal, India; #Equal contribution

Email

Amal Kumar Bandyopadhyay - *E-mail: akbanerjee@biotech.buruniv.ac.in; *Corresponding author

Article Type

Software

Date

Received December 3, 2018; Accepted December 6, 2018; Published December 22, 2018

Global minimal structure of protein/enzyme is energetically compromised that maintains an intricate balance between the rigidity and the flexibility. Such a state makes it interactive to its ligand molecules. Although protein data bank files (PDB) may have achieved the state, in many situations minimization has been crucial to overcome unwanted steric clashes, and other conformational strains. It is more so, when orthologous PDB structures that are intended in a given study, show variations in resolution, R-factor, shell-water contents, loop characteristics etc. Here, a fully automated procedure of minimization would be highly useful. AUTOMINv1.0 is such an automation of minimization that runs on any number of structure files with any number of chains in them along with the inclusion of selective/non-selective shell-waters interacting with polar and or non-polar atom-types of protein. Comparison of the mean binary items of salt-bridges of minimized and un-minimized structures (chains > 100) of nucleoside diphosphate kinase from mimi virus shows dramatic improvements in the earlier. Again, the mean steric clashes of 2AZ3.pdb are reduced upon minimization. Remarkably,
the observed steric clashes between shell-waters and atom-types of protein are seen to be removed upon minimization. Taken together, AUTOMINv1.0 is an automation of minimization that finds applications in structural bioinformatics.

Keywords

Automation; minimization; shell-water, CHARMM, Salt-bridge, steric clash

Citation

Ul Islam et al. Bioinformation 14(9): 525-529 (2018)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.