UCSF Chimera statistics

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Citations per year

Number of citations per year for the bioinformatics software tool UCSF Chimera
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Tool usage distribution map

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

This word cloud represents UCSF Chimera usage per disease context
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Popular tool citations

chevron_left Protein-ligand docking 3D macromolecule reconstruction Molecule viewers Structure visualization Multiple amino acid sequence alignment Pairwise sequence alignment chevron_right
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Protocols

UCSF Chimera specifications

Information


Unique identifier OMICS_03803
Name UCSF Chimera
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/UCSF_Chimera

Versioning


No version available

Maintainer


  • person_outline Thomas E. Ferrin

Additional information


Tuto: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html

Publication for UCSF Chimera

UCSF Chimera citations

 (1286)
library_books

Structural basis for the recognition of complex type N glycans by Endoglycosidase S

2018
Nat Commun
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] Supplementary Table . Atomic coordinates and structure factors have been deposited with the Protein Data Bank, accession code 6EN3. Molecular graphics and structural analyses were performed with the UCSF Chimera package. […]

call_split

Structural and immunologic correlates of chemically stabilized HIV 1 envelope glycoproteins

2018
PLoS Pathog
PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986
call_split See protocol

[…] An initial model was generated based on PDB ID 5CEZ [] and PDB ID 3SE9 [] using UCSF Chimera [], Modeler [] and Coot []. A library of 200 homologous 7-mer peptide fragment coordinates per relevant residue were compiled and used in iterative centroid-representation density-guided […]

library_books

Analysis of β tubulin carbendazim interaction reveals that binding site for MBC fungicides does not include residues involved in fungicide resistance

2018
Sci Rep
PMCID: 5940828
PMID: 29740047
DOI: 10.1038/s41598-018-25336-5

[…] king). The docking was performed using the ‘Accurate’ parameter at otherwise default parameters, with no region of interest defined (blind docking). Modeling and docking results were visualized using UCSF Chimera v1.12 software. […]

library_books

Structure and mechanism of the two component α helical pore forming toxin YaxAB

2018
Nat Commun
PMCID: 5935710
PMID: 29728606
DOI: 10.1038/s41467-018-04139-2

[…] del.The native YaxB dataset was recorded at 4 Å resolution and phased by molecular replacement on the PaxB crystal structure (Chain A). Homology modeling was performed with MODELER interfaced through UCSF Chimera and the obtained coordinates applied for Patterson search calculations in Phaser. Though appropriate rotation solutions were achieved, the full-length model was unable to be positioned in […]

library_books

Probing biological activity through structural modelling of ligand receptor interactions of 2,4 disubstituted thiazole retinoids

2018
PMCID: 5933457
PMID: 29439915
DOI: 10.1016/j.bmc.2018.02.002

[…] The docked structures of each ligand with the three isoforms of RAR were used as starting models. Any remaining solvent molecules were removed. Missing loops were built with MODELLER (v9.19), via UCSF Chimera. The final protein structures covered residues 182–415 for RARα, 182–411 for RARβ, and 188–419 for RARγ.The ligands were parameterised using Gasteiger point charges in the AMBER ff99sb fo […]

library_books

An effector from the Huanglongbing associated pathogen targets citrus proteases

2018
Nat Commun
PMCID: 5928222
PMID: 29712915
DOI: 10.1038/s41467-018-04140-9

[…] ng the default settings. The template used for CsSAG12-1 was CysEP from Ricinus communis (RCSB Protein Data Bank ID 1S4V) with 56% sequence identity. Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR-01081). The Chimera interactive graphics […]


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UCSF Chimera institution(s)
Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA

UCSF Chimera review

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krawutzi

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Desktop
Very useful and intuitive program, commandline is available and tight integration with python