These refinements started with YASARA generated initial refinement [9-11, 13].
Each model was exported to the following formats: Maestro (MAE) and YASARA (PDB).
Our research team, in collaboration with HudsonAlpha Institute for Biotechnology is working to establish a work flow that uses programs such as YASARA
to make in silico three-dimensional models of transcription factors such as LEF1 (Lymphoid enhancer-binding factor 1) and SP100 (Nuclear autoantigen Sp-100).
The WT and mutant models were visualized using Foldx plugin in YASARA
. The stability of the mutant protein structure was predicted by Foldx in YASRA software (an empirical force field-based protein design algorithm) and changes in protein stability and dynamics after mutation were evaluated .
Vriend, "Increasing the precision of comparative models with YASARA
NOVA--a self-parameterizing force field," Proteins: Structure, Function and Genetics, vol.
We modeled the AA exchanges at 156 on the HLA-A*24:02 structure (PDB 3I6L)  using the Site Directed Mutator (SDM) server (http://mordred.bioc.cam .ac.uk/sdm/sdm.php)  and the FoldX plugin for Yasara
After that, the structure was relaxed with YASARA
Energy minimization was performed using YASARA
Server of Protein Energy minimization (10).
By using the predictive computational force field FoldX (11) in YASARA
(12), we modeled the effects on structural stability of I117V, I117M, H275Y, I117V + H275Y, and I117M + H275Y mutations in the pandemic (H1N1) 2009 NA crystal structure (Protein Data Bank no.