Computational protocol: Identification of a novel prostate cancer susceptibility variant in the KLK3 gene transcript

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Protocol publication

[…] Potential conformations of the original and mutated crystal structure models were investigated using energy minimisation and force field (Goodford ). To gain further insights into the effects of substitution at Ile179 we simulated solvated Ile179 and Ile179Thr. Structure files were generated using Visual Molecular Dynamics (VMD) (Humphrey et al. ). The system was equilibrated using Nanoscale Molecular Dynamics (NAMD) (Phillips et al. ) and simulated using ACEMD (Giupponi et al. ) with the Chemistry at HARvard Molecular Mechanics (CHARMM) (Brooks et al. ) force field. Ten independent simulations were carried out for both variants which were then analysed to determine the models’ average energies. […]

Pipeline specifications

Software tools VMD, NAMD, CHARMM
Application Protein structure analysis
Diseases Neoplasms, Prostatic Neoplasms
Chemicals Calcium, Nucleotides