PyMOL protocols

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PyMOL computational protocol

PyMOL specifications

Information


Unique identifier OMICS_03802
Name PyMOL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/PyMOL

Subtool


  • PyKnot

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Documentation


Maintainers


  • person_outline Rhold C. Lua <>
  • person_outline Thomas Holder <>

Publication for PyMOL

PyMOL IN pipelines

 (173)
2018
PMCID: 5788867
PMID: 29379064
DOI: 10.1038/s41598-018-20137-2

[…] performed using z-dock, a total of 2000 poses were generated15. the top 500 docking poses, as scored by z-rank, were chosen for an r-dock refinement16. next, the refined poses were visualized using pymol. all the dockings where the catalytic site of trypsin17 and the proteolytic sites (r or k) of the hev proteins were not within the docking interface, were ruled out. the docking poses […]

2018
PMCID: 5796906
PMID: 29434596
DOI: 10.3389/fimmu.2018.00075

[…] were harmonically constrained using the lincs method. periodic boundary conditions were applied, and trajectories were saved every 2 ps. data analysis was performed using xmgrace,1 vmd 1.9.2 (31), pymol 1.7 (schrödinger, llc, new york, ny, usa), dsv 4.0, and other analysis programs available in gromacs. the area per lipid (apl) was calculated using gridmat-md (32)., the binding free energies […]

2018
PMCID: 5834254
PMID: 29541398
DOI: 10.18632/oncotarget.24323

[…] authors., initial model of the chimeric reporter was built using the i-tasser server [63]. manual modeling operations were performed in coot [64] and molecular graphics were generated in pymol [65] [available at: http://www.pymol.org]., the primers were synthesized and page purified by idt dna. fugene 6 transfection reagent was purchased from promega while lipofectamine rnaimax […]

2018
PMCID: 5834254
PMID: 29541398
DOI: 10.18632/oncotarget.24323

[…] the chimeric reporter was built using the i-tasser server [63]. manual modeling operations were performed in coot [64] and molecular graphics were generated in pymol [65] [available at: http://www.pymol.org]., the primers were synthesized and page purified by idt dna. fugene 6 transfection reagent was purchased from promega while lipofectamine rnaimax was from life technologies/invitrogen. […]

2018
PMCID: 5842395
PMID: 29718486
DOI: 10.1093/jisesa/iey011

[…] template was identified from pdb by a locally installed lomets meta-threading server. models were constructed by iterative tasser simulations. the generated pdb files were then visualized with pymol molecular graphics system., to investigate the transcriptional changes of ctls during the various stages of o. furnacalis, total rna samples were individually prepared from three different […]

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