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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Biomedical Informatics
2018
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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 |
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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 |
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