http://orcid.org/0000-0001-5469-3170
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Abstract
| Abbreviations | ||
| SAHA | = | suberoylanilide hydroxamic acid |
| EhHDAC | = | Histone Deacetylase from Entamoeba histolytica |
| Rg | = | Radius of gyration |
| RMSD | = | root-mean-square deviation |
| RMSF | = | root-mean-square fluctuation |
| MDS | = | molecular dynamics simulation |
| VMD | = | Visual Molecular Dynamics |
| NAMD | = | Nanoscale Molecular Dynamics |
| PBC | = | periodic boundary conditions |
| PME | = | Particle Mesh Ewald |
| 3D | = | three-dimensional |
| Cα | = | alpha carbon |
| FDA | = | Food and Drug Administration |
| ns | = | nanoseconds |
| GPU CUDA | = | Graphics Processing Unit Compute Unified Device Architecture |
Communicated by Ramaswamy H. Sarma
Acknowledgements
The authors thank Héctor Oliver-Hernández for art work support. We are also grateful to LANCAD for the supercomputer time support. The MD simulation was performed in the Laboratory of Bioinformatics at FCQB-UAS and in the Hybrid Cluster Xiuhcoatl (http://clusterhibrido.cinvestav.mx) at CINVESTAV-IPN, México.
Disclosure statement
The funders had no role in the study design, data collection and analysis, preparation of the manuscript or decision to publish.