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PCASSO specifications

Information


Unique identifier OMICS_19687
Name PCASSO
Alternative name Protein C-Alpha Secondary Structure Output
Interface Web user interface
Restrictions to use None
Input data Some Cα atoms, PDB structures or MD simulation trajectories.
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Charles Brooks

Additional information


http://brooks.chem.lsa.umich.edu/index.php?pcassoserver=submit

Information


Unique identifier OMICS_19687
Name PCASSO
Alternative name Protein C-Alpha Secondary Structure Output
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some Cα atoms, PDB structures or MD simulation trajectories.
Input format PDB
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Registration required Yes
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Charles Brooks

Additional information


http://brooks.chem.lsa.umich.edu/index.php?pcassoserver=submit

Publication for Protein C-Alpha Secondary Structure Output

PCASSO citations

 (3)
library_books

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments

2016
Int J Mol Sci
PMCID: 4813195
PMID: 26978354
DOI: 10.3390/ijms17030333

[…] d secondary structure assignment program from Cα fragments assigned by DSSP. Rare fragments can be detected using our outlier fragments detection. In a large-scale comparison of 11 available methods, PCASSO agrees most with DSSP, followed by SACF, KAKSI and PROSS, with both PCASSO and SACF preferring to reduce residues at the N cap and C cap regions of helices and β-sheets if DSSP is taken as the […]

library_books

Using diffusion of innovation theory to understand the factors impacting patient acceptance and use of consumer e health innovations: a case study in a primary care clinic

2015
PMCID: 4391079
PMID: 25885110
DOI: 10.1186/s12913-015-0726-2

[…] making processes [,,]. Currently, a substantial amount of e-health initiatives are in either the development or implementation phase [,], such as the Patient-Centered Access to Secure Systems Online (PCASSO) in the United States [], or “Personally Controlled Electronic Health Record” (PCEHR), which is being implemented by the National E-Health transaction Authority (NETHA) in Australia []. Accordi […]

library_books

Predicting Protein Backbone Chemical Shifts From Cα Coordinates: Extracting High Resolution Experimental Observables from Low Resolution Models

2014
J Chem Theory Comput
PMCID: 4295808
PMID: 25620895
DOI: 10.1021/ct5009125

[…] The distance-based structural features used to predict backbone chemical shifts from Cα coordinates were identical to those recently used by the program PCASSO to assign protein secondary structure from Cα coordinates. Briefly, for a given residue, i, a set of 43 features are calculated from the Cα coordinates and the pseudocenter coordinates, respect […]

Citations

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PCASSO institution(s)
Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Department of Biophysics Program, University of Michigan, Ann Arbor, MI, USA
PCASSO funding source(s)
Supported by NIH through GM037554 and NSF through funding from the Center for Biological Physics (PHY0216576); and by the University of Michigan President’s Postdoctoral Fellowship.

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