gmf12
Postdoctoral researcher at the Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo
Pinned Repositories
plpronalysis
SARS-COV-2 papain-like protease: Accessibility of the inhibitor is promoted by BL2-loop region
FXR-RXR_analysis
Allosteric signal transduction in FXR/RXR heterodimers bound to steroidal antagonists
LDLR-analysis
LDLR + membrane simularions
NR_MSM
Allosteric signal transduction in FXR/RXR heterodimers bound to steroidal antagonists
pcaanalysismrpo
SARS-COV-2 Mpro conformational changes induced by covalently bound ligands
PCSK9-analysis
Principal Component Analysis (PCA) was used to generate the amino acid backbone of PCSK9 (pro-domain, catalytic, CHR domain and LDLR-EGF-). The pro-domain (Chain P), Catalytic and CHR domain (Chain A) and LDLR-EGF- (Chain E) and backbone atoms of each frame were extracted and aligned using scripts (trj_selection_dl.py and trj_align.py) from Schrodinger package 2019v.4. Individual simulations from all runs were merged using the trj_merge.py script into a final trajectory and CMS file, which was further used to generate the principal components. Principal components of protein backbone atoms were calculated using the trj_essential_dynamics.py script.
SurA
gmf12's Repositories
gmf12/SurA
gmf12/FXR-RXR_analysis
Allosteric signal transduction in FXR/RXR heterodimers bound to steroidal antagonists
gmf12/NR_MSM
Allosteric signal transduction in FXR/RXR heterodimers bound to steroidal antagonists
gmf12/plpronalysis
SARS-COV-2 papain-like protease: Accessibility of the inhibitor is promoted by BL2-loop region
gmf12/LDLR-analysis
LDLR + membrane simularions
gmf12/PCSK9-analysis
Principal Component Analysis (PCA) was used to generate the amino acid backbone of PCSK9 (pro-domain, catalytic, CHR domain and LDLR-EGF-). The pro-domain (Chain P), Catalytic and CHR domain (Chain A) and LDLR-EGF- (Chain E) and backbone atoms of each frame were extracted and aligned using scripts (trj_selection_dl.py and trj_align.py) from Schrodinger package 2019v.4. Individual simulations from all runs were merged using the trj_merge.py script into a final trajectory and CMS file, which was further used to generate the principal components. Principal components of protein backbone atoms were calculated using the trj_essential_dynamics.py script.
gmf12/pcaanalysismrpo
SARS-COV-2 Mpro conformational changes induced by covalently bound ligands