SpacePAC specifications

Information


Unique identifier OMICS_19678
Name SpacePAC
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.18.3
Stability Stable
Requirements
BiocGenerics, R(>=2.15), RUnit, rgl, iPAC
Maintained Yes

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Documentation


Maintainers


  • person_outline Hongyu Zhao <>
  • person_outline Gregory Ryslik <>

Publication for SpacePAC

SpacePAC in publications

 (2)
PMCID: 5260099
PMID: 28115009
DOI: 10.1186/s13073-016-0393-x

[…] studied enrichment of mutations in protein-protein interaction interfaces. structman [] annotated the amino acid variations of single-nucleotide polymorphisms (snps) in the context of 3d structures. spacepac [], mutation3d [], hotmaps [], and hotspot3d [] used 3d structures to identify mutational clusters in cancer. these efforts have generated interesting sets of candidate functional mutations […]

PMCID: 4213513
PMID: 25360158
DOI: 10.1186/s13073-014-0081-7

[…] information. using these data, they developed the inca classifier model to predict cancer-related mutations with 83% specificity and 77% sensitivity. ryslik et al. [] developed an approach, spacepac (spatial protein amino acid clustering), to identify mutational clustering by directly considering the protein tertiary structure in 3d space. utilizing the mutational data from the cosmic […]


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SpacePAC institution(s)
Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA; Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Yale Center for Medical Informatics, Yale School of Medicine, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
SpacePAC funding source(s)
Supported in part by NSF Grant DMS 1106738, NIH Grants GM59507 and CA154295, and GM102869.

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