PyMOL statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PyMOL

Tool usage distribution map

This map represents all the scientific publications referring to PyMOL per scientific context
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Associated diseases

This word cloud represents PyMOL usage per disease context

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PyMOL specifications


Unique identifier OMICS_03802
Name PyMOL
Alternative name AxPyMol
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


  • PyKnot




No version available



  • person_outline Rhold C. Lua
  • person_outline Thomas Holder

Publication for PyMOL

PyMOL citations


Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo Blood Group Antigen Binding Profiles

PMCID: 5964351
DOI: 10.1128/mBio.00869-18
call_split See protocol

[…] nce was determined by the use of the Modeller platform from the Bioinformatics Toolkit from the Max Planck Institute using GII.4.2012/NSW0514 as the template (). Dimeric models were created using The PyMOL Molecular Graphics System, version (Schrödinger, LLC). […]


High resolution AFM structure of DNA G wires in aqueous solution

Nat Commun
PMCID: 5958085
PMID: 29773796
DOI: 10.1038/s41467-018-04016-y

[…] ained dynamics with constraints of 5, 4, 3, 2, 1, and 0.5 kcal mol−1 Å−2. Finally, simulations were run unrestrained at 1 atm and 300 K for a duration of 1 ns. Molecules were visualized using VMD and Pymol. Molecular structures were averaged over the 1 ns unrestrained simulation and used for AFM simulations. […]


X ray structure of a carpet like antimicrobial defensin–phospholipid membrane disruption complex

Nat Commun
PMCID: 5958116
PMID: 29773800
DOI: 10.1038/s41467-018-04434-y
call_split See protocol

[…] d Rfree values of 0.2031 and 0.2519, respectively. All data collection and refinement statistics are summarized in Table . All programs were accessed via the SBGrid suite. Figures were prepared using PyMol. Movies were prepared using Chimera. […]


Structure guided Discovery of Dual recognition Chemibodies

Sci Rep
PMCID: 5954141
PMID: 29765112
DOI: 10.1038/s41598-018-25848-0
call_split See protocol

[…] re of rat DPP-IV with Fab 11A19 (PDB code: 4FFV) as a search model. Model building and refinement were carried out in COOT and REFMAC in CCP4, respectively. All structural figures were prepared using PyMOL (Schrodinger Inc, San Diego, CA). […]


CHAT gene polymorphism rs3810950 is associated with the risk of Alzheimer’s disease in the Czech population

J Biomed Sci
PMCID: 5950140
PMID: 29759072
DOI: 10.1186/s12929-018-0444-2
call_split See protocol

[…] p:// and homology modelling software MODELLER []. Search for hydrogen bond network was done via VMD [], Schrodinger Maestro software (Schrodinger, L. Biologics Suite 2017–1) and PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.) as well as the visualization device. […]


Computer aided design of amino acid based therapeutics: a review

Drug Des Devel Ther
PMCID: 5958949
DOI: 10.2147/DDDT.S159767

[…] shown in . The X-ray crystallographic structures of Aldesleukin (PDB ID: 1M47; ) and Leuprolide (PDB ID: 1YY2; ) were obtained from the Protein Data Bank (PDB; and visualized by PyMol tool. The structure of Spaglumic acid was retrieved (in MOL format) from PubChem database ( with the PubChem ID 188803 () and visualized using PyMol. Aldesleuki […]

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