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Rout AK, Paramanik S, Dehury B, Acharya V, Swain HS, Pradhan SK, Behera B, Pati SK, Behera BK, Das BK. Elucidating the molecular interaction of Zebrafish (Danio rerio) peptidoglycan recognition protein 2 with diaminopimelic acid and lysine type peptidoglycans using in silico approaches. J Biomol Struct Dyn 2019; 38:3687-3699. [DOI: 10.1080/07391102.2019.1666742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sunanda Paramanik
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Budheswar Dehury
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Varsha Acharya
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Himanshu Sekhar Swain
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Bhaskar Behera
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore, India
| | - Soumen Kumar Pati
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, India
| | - Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Basanta Kumar Das
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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