Cargando…

POWAINDv1.0: A Program for Protein-Water Interactions Determination

Protein is the most exposed biomolecule in the aqueous environment of the cell. Its structure maintains a delicate balance between the rigidity and the flexibility that imparts binding specificity to its substrate/ligand, etc. Intramolecular interactions of polar and non-polar groups of amino acid r...

Descripción completa

Detalles Bibliográficos
Autores principales: Banerjee, Sahini, Mondal, Buddhadev, Islam, Rifat Nawaz Ul, Gupta, Parth Sarthi Sen, Mitra, Debanjan, Bandyopadhyay, AmalKumar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563665/
https://www.ncbi.nlm.nih.gov/pubmed/31223212
http://dx.doi.org/10.6026/97320630014530
_version_ 1783426583650893824
author Banerjee, Sahini
Mondal, Buddhadev
Islam, Rifat Nawaz Ul
Gupta, Parth Sarthi Sen
Mitra, Debanjan
Bandyopadhyay, AmalKumar
author_facet Banerjee, Sahini
Mondal, Buddhadev
Islam, Rifat Nawaz Ul
Gupta, Parth Sarthi Sen
Mitra, Debanjan
Bandyopadhyay, AmalKumar
author_sort Banerjee, Sahini
collection PubMed
description Protein is the most exposed biomolecule in the aqueous environment of the cell. Its structure maintains a delicate balance between the rigidity and the flexibility that imparts binding specificity to its substrate/ligand, etc. Intramolecular interactions of polar and non-polar groups of amino acid residues and intermolecular weak interactions between these groups and shell-waters may contribute to the overall stability of the tertiary structure. However, the question as to what are the dynamics of interactions of shell-water with respect to weak forces and atom-groups of protein (AGP), requires systematic investigations. In this end, we have developed a procedure POWAINDv1.0 that analyzes interactions of crystallographic shell-waters (CSH) in residues and AGP specific manner. The shell-water and AGP specific bridge-interactions are also extracted. Further, the program analyzes favorable and unfavorable nature of each interaction based on the actual and 75% of the sum of van der Waals (vdW) radii of interacting atoms. The EXCEL-outputs are useful in understanding the profile for AGP-CSH interactions and contribution of each component in AGP. Taken together, the program provides intricate details on CSHprotein interactions and finds application in the structural Bioinformatics
format Online
Article
Text
id pubmed-6563665
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher Biomedical Informatics
record_format MEDLINE/PubMed
spelling pubmed-65636652019-06-20 POWAINDv1.0: A Program for Protein-Water Interactions Determination Banerjee, Sahini Mondal, Buddhadev Islam, Rifat Nawaz Ul Gupta, Parth Sarthi Sen Mitra, Debanjan Bandyopadhyay, AmalKumar Bioinformation Software Protein is the most exposed biomolecule in the aqueous environment of the cell. Its structure maintains a delicate balance between the rigidity and the flexibility that imparts binding specificity to its substrate/ligand, etc. Intramolecular interactions of polar and non-polar groups of amino acid residues and intermolecular weak interactions between these groups and shell-waters may contribute to the overall stability of the tertiary structure. However, the question as to what are the dynamics of interactions of shell-water with respect to weak forces and atom-groups of protein (AGP), requires systematic investigations. In this end, we have developed a procedure POWAINDv1.0 that analyzes interactions of crystallographic shell-waters (CSH) in residues and AGP specific manner. The shell-water and AGP specific bridge-interactions are also extracted. Further, the program analyzes favorable and unfavorable nature of each interaction based on the actual and 75% of the sum of van der Waals (vdW) radii of interacting atoms. The EXCEL-outputs are useful in understanding the profile for AGP-CSH interactions and contribution of each component in AGP. Taken together, the program provides intricate details on CSHprotein interactions and finds application in the structural Bioinformatics Biomedical Informatics 2018-12-22 /pmc/articles/PMC6563665/ /pubmed/31223212 http://dx.doi.org/10.6026/97320630014530 Text en © 2018 Biomedical Informatics http://creativecommons.org/licenses/by/3.0/ 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.
spellingShingle Software
Banerjee, Sahini
Mondal, Buddhadev
Islam, Rifat Nawaz Ul
Gupta, Parth Sarthi Sen
Mitra, Debanjan
Bandyopadhyay, AmalKumar
POWAINDv1.0: A Program for Protein-Water Interactions Determination
title POWAINDv1.0: A Program for Protein-Water Interactions Determination
title_full POWAINDv1.0: A Program for Protein-Water Interactions Determination
title_fullStr POWAINDv1.0: A Program for Protein-Water Interactions Determination
title_full_unstemmed POWAINDv1.0: A Program for Protein-Water Interactions Determination
title_short POWAINDv1.0: A Program for Protein-Water Interactions Determination
title_sort powaindv1.0: a program for protein-water interactions determination
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563665/
https://www.ncbi.nlm.nih.gov/pubmed/31223212
http://dx.doi.org/10.6026/97320630014530
work_keys_str_mv AT banerjeesahini powaindv10aprogramforproteinwaterinteractionsdetermination
AT mondalbuddhadev powaindv10aprogramforproteinwaterinteractionsdetermination
AT islamrifatnawazul powaindv10aprogramforproteinwaterinteractionsdetermination
AT guptaparthsarthisen powaindv10aprogramforproteinwaterinteractionsdetermination
AT mitradebanjan powaindv10aprogramforproteinwaterinteractionsdetermination
AT bandyopadhyayamalkumar powaindv10aprogramforproteinwaterinteractionsdetermination