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Jmol specifications

Information


Unique identifier OMICS_05004
Name Jmol
Alternative names Jmol application, JSmol
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 14.20.5
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Jmol

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Miguel Howard

Additional information


http://jmol.sourceforge.net/docs/

Information


Unique identifier OMICS_05004
Name Jmol
Alternative names Jmol application, JSmol
Interface Web user interface, Application programming interface
Restrictions to use None
Programming languages Javascript
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Requirements
JRE
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Jmol

Documentation


Maintainer


  • person_outline Miguel Howard

Additional information


http://jmol.sourceforge.net/docs/

Jmol citations

 (103)
call_split

KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking

2018
J Cheminform
PMCID: 5891443
PMID: 29633047
DOI: 10.1186/s13321-018-0274-y
call_split See protocol

[…] s of docking scores, running our program multiple times and examining the binding poses of a ligand would be recommended. The docking conformations of original and mutant kinases are visualized using JSmol (http://wiki.jmol.org/index.php/JSmol) to highlight the structural consequence of the mutation (Fig. b). Users can download these conformations for further structural comparisons.Fig. 2 […]

call_split

Inhibition of Protein Aggregation by Several Antioxidants

2018
PMCID: 5889867
PMID: 29765505
DOI: 10.1155/2018/8613209
call_split See protocol

[…] s representative. In other words, only the minimum energy conformation states of the ligand-bound protein complex out of many generated binding modes were considered. Binding modes were visualized in JSmol, and PDB was used for the identification of residues involved in binding. […]

library_books

Nilotinib impairs skeletal myogenesis by increasing myoblast proliferation

2018
PMCID: 5819301
PMID: 29463296
DOI: 10.1186/s13395-018-0150-5

[…] formed based on the conformations found in the corresponding ligand–protein crystal structures (PDB entry 3GP0). MAPK11 (p38β) protein structure in a complex with Nilotinib is represented in 3D using JSmol, an open-source Java viewer for chemical structures in 3D (http://www.jmol.org/). The modeled structure and sequence can be downloaded in PDB (PDB ID: 3GP0) and FASTA formats, respectively. The […]

library_books

Investigation and identification of functional post translational modification sites associated with drug binding and protein protein interactions

2017
BMC Syst Biol
PMCID: 5763307
PMID: 29322920
DOI: 10.1186/s12918-017-0506-1

[…] file : Table S2). The spatial amino acid compositions were obtained by computing the relative frequencies of the 20 amino acids within 2 to 12 Å radial distances of the modified residues. Next, using JSmol software [], neighboring amino acids at the sequence level and in the spatial context were presented with different colors on the PDB 3D structures for the structural characterization of PTM sub […]

library_books

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

2017
Nucleic Acids Res
PMCID: 5753225
PMID: 29126160
DOI: 10.1093/nar/gkx1070

[…] e PDBe REST API has been integrated into various external tools and services, such as the Volume Slicer () for Electron Microscopy Data Bank (EMDB; ()) entries, LiteMol (Sehnal et al. in press), Jmol/JSmol () and Coot () to display SIFTS mappings and/or validation information, and JalView () to directly query PDB data from the viewer. […]

library_books

Caspase 8, association with Alzheimer’s Disease and functional analysis of rare variants

2017
PLoS One
PMCID: 5630132
PMID: 28985224
DOI: 10.1371/journal.pone.0185777

[…] 3 residues (97% coverage of the submitted Ser202-Asp359 sequence) and 176 residues (99% coverage of the submitted Met1-Asp177 sequence) were modelled with 100% confidence. Models were depicted in the JSmol molecular viewer. […]

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