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



Rifat Nawaz Ul Islam$,1, Debanjan Mitra$,2, Parth Sarthi Sen Gupta$,3, Sahini Banerjee$,4,
Buddhadev Mondal$,5, Amal Kumar Bandyopadhyay2,*



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



Amal Kumar Bandyopadhyay - *E-mail:; *Corresponding author


Article Type




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.



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



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


Edited by

P Kangueane






Biomedical Informatics



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.