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Cancer3D specifications

Information


Unique identifier OMICS_30514
Name Cancer3D
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes

Maintainers


  • person_outline Adam Godzik
  • person_outline Thomas Hrabe

Additional information


The version 1 of the database is still available at http://old.cancer3d.org/ http://www.cancer3d.org/tutorial

Publications for Cancer3D

Cancer3D citations

 (3)
library_books

Mapping genetic variations to three dimensional protein structures to enhance variant interpretation: a proposed framework

2017
Genome Med
PMCID: 5735928
PMID: 29254494
DOI: 10.1186/s13073-017-0509-y

[…] genetic variations and protein structure are not always easy to find. A few computational tools have begun to emerge (cBioPortal [], COSMIC-3D [], CRAVAT [], Jalview [], MuPIT [], MutDB [], STRUM [], Cancer3D []) that enable users to take individual genetic variations, or a list of them, and visualize these in the context of protein structures. For example, CRAVAT [] allows a user to upload a vari […]

library_books

Spatial distribution of disease associated variants in three dimensional structures of protein complexes

2017
Oncogenesis
PMCID: 5623905
PMID: 28945216
DOI: 10.1038/oncsis.2017.79

[…] such loci contain at least one nsSNV with a high predicted functional impact. Meta-methods and databases that combine several prediction tools using statistical learning have also been developed., , Cancer3D maps nsSNVs from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE) onto 3D structures of the corresponding proteins and annotates them with respect to predicted canc […]

library_books

Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics

2015
PLoS Comput Biol
PMCID: 4287345
PMID: 25568936
DOI: 10.1371/journal.pcbi.1004024

[…] d within) a Pfam domain. Note also that these numbers refer to PFRs in all known protein isoforms according to ENSEMBL v72. While the results for all these PFR-Drug pairs can be browsed at http://www.cancer3d.org , in this manuscript we only discuss results obtained for the largest isoform of each protein (). A similar protocol to assign protein functional regions was used in our previous publicat […]


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Cancer3D institution(s)
Bioinformatics and Systems Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA; Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA; Barcelona Supercomputing Centre, Barcelona, Spain
Cancer3D funding source(s)
Supported by SBP funds and NIH grant GM118187.

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