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Protocols

g_mmpbsa specifications

Information


Unique identifier OMICS_11517
Name g_mmpbsa
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data The output from the tool is used further as input in python scripts which is provided in this package, to get the final binding energy and energetic contribution of each residue.
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 5.1.2
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Andrew Lynn

Publications for g_mmpbsa

g_mmpbsa citations

 (70)
library_books

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses

2018
BMC Genomics
PMCID: 5954268
PMID: 29764421
DOI: 10.1186/s12864-018-4461-z

[…] the SA method, computed as:3ΔGsolv=ΔGsolv,polar+ΔGsolv,nonpolarThe binding free energy and decomposed interaction energy between residues of HA protein and receptor analogs were calculated using the g_mmpbsa package []. […]

call_split

Deciphering the binding behavior of flavonoids to the cyclin dependent kinase 6/cyclin D complex

2018
PLoS One
PMCID: 5929560
PMID: 29715320
DOI: 10.1371/journal.pone.0196651
call_split See protocol

[…] ng the MD trajectory at an interval of 20ps, and then were employed for binding free energy analysis. The MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) method, which was implemented in g_mmpbsa tool[, ], was performed to compute the binding free energies of the inhibitors binding to CDK6/cyclin D complex. In this method, the binding free energy was calculated with the following equa […]

library_books

Probing biological activity through structural modelling of ligand receptor interactions of 2,4 disubstituted thiazole retinoids

2018
PMCID: 5933457
PMID: 29439915
DOI: 10.1016/j.bmc.2018.02.002

[…] straints at a 2 fs timestep, with Parinello-Rahman barostat at 1 bar. Finally, position restraints were released and two parallel production MD simulations were conducted for a 10 ns time period. The g_mmpbsa package was used to calculate binding energies between ligand and protein, and to quantify per-residue contributions to binding. The final 2 ns of converged simulation time was used for each […]

call_split

Molecular dynamics simulation (MDS) analysis of Vibrio cholerae ToxT virulence factor complexed with docked potential inhibitors

2018
Bioinformation
PMCID: 5953856
DOI: 10.6026/97320630014101
call_split See protocol

[…] icle-Mesh Ewald method was used to calculate Long-range electrostatic interactions. The MD runs were carried out in the NPT ensemble (50 ns) for each system. The binding affinities were calculated by g_mmpbsa package []. […]

library_books

Computational Insight Into the Structural Organization of Full Length Toll Like Receptor 4 Dimer in a Model Phospholipid Bilayer

2018
Front Immunol
PMCID: 5857566
PMID: 29593733
DOI: 10.3389/fimmu.2018.00489

[…] mann equation and solvent accessible surface area methods. The entropic contribution, TS (absolute temperature T multiplied by entropy S), is generally estimated by normal mode analysis. However, the g_mmpbsa program (, ), which we used for binding free energy calculation, ignores entropic contribution to improve computational efficiency. In computational binding free energy calculations, the comp […]

library_books

Zerumbone reduces proliferation of HCT116 colon cancer cells by inhibition of TNF alpha

2018
Sci Rep
PMCID: 5840388
PMID: 29511228
DOI: 10.1038/s41598-018-22362-1

[…] and MD simulation trajectory analysis, the binding free-energy (ΔGbind) calculations were carried out for the 30 ns simulated complexes of the 5MU8-Zerumbone complex and 5MU8-α-humulene complex using g_mmpbsa (http://rashmikumari.github.io/g_mmpbsa/). The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) estimates the free energy interactions as defined by Kollman et al.. The equation o […]

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g_mmpbsa institution(s)
School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India; CSIR Open Source Drug Discovery Unit, Anusandhan Bhavan, Delhi, India

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