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Protocols

PCSB specifications

Information


Unique identifier OMICS_33465
Name PCSB
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Programming languages Java
Computer skills Medium
Stability No
Requirements
Java Runtime Environment
Maintained No

Subtool


  • AFDP

Versioning


No version available

Publication for PCSB

PCSB citations

 (6)
library_books

Flatworms have lost the right open reading frame kinase 3 gene during evolution

2015
Sci Rep
PMCID: 4894443
PMID: 25976756
DOI: 10.1038/srep09417

[…] praisal of the nucleotide binding site and possible protein-ligand interactions was undertaken by visual inspection of structures in Coot as well as distance analyses using in-house scripts (AH) from PCSB software. Sequences of domains that displayed differences in the alignment between parasitic flatworms and human RIOK-1s were compared using MUSCLE-guided alignments and displayed using the progr […]

library_books

An integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements

2014
3 Biotech
PMCID: 4327748
PMID: 28324365
DOI: 10.1007/s13205-014-0222-0

[…] for structural biology, the algorithm appears not to have been ported to other programming languages.In the context of our Java programme collection for structural biology and biophysical chemistry (PCSB) (Hofmann and Wlodawer ), and specifically for the application SBAL (Wang et al. ), a tool for structure-based sequence alignments, we have implemented the DSSP algorithm as described in the orig […]

call_split

SDAR: a practical tool for graphical analysis of two dimensional data

2012
BMC Bioinformatics
PMCID: 3480940
PMID: 22892030
DOI: 10.1186/1471-2105-13-201
call_split See protocol

[…] SDAR is a Java application that builds on and extends fundamental Java classes developed within the Program Collection for Structural Biology and Biophysical Chemistry (PCSB) []. The four PCSB components of the program are the main class providing the GUI, a class to describe the Dataseries objects, a JPanel class GraphPanel that provides plotting functionality, and […]

library_books

Phosphorylation of CRN2 by CK2 regulates F actin and Arp2/3 interaction and inhibits cell migration

2012
Sci Rep
PMCID: 3268813
PMID: 22355754
DOI: 10.1038/srep00241

[…] taset ρ* = 18 mg ml−1 was used to fit the atomic model of the triple phosphorylated coiled coil peptide from the MD simulation (see above). Model fitting was performed with the program SAFIR from the PCSB collection; theoretical scattering curves and their fit to experimental data were obtained with CRYSOL. […]

library_books

Divalent Cations and Redox Conditions Regulate the Molecular Structure and Function of Visinin Like Protein 1

2011
PLoS One
PMCID: 3206844
PMID: 22073194
DOI: 10.1371/journal.pone.0026793

[…] n of 30 nM using a Hamilton syringe extending beneath the barrier. The surface pressure π was recorded as a function of time for ∼45 min. Adsorption data were analysed with the software SDAR from the PCSB program collection . […]

call_split

Insights into the Membrane Interactions of the Saposin Like Proteins Na SLP 1 and Ac SLP 1 from Human and Dog Hookworm

2011
PLoS One
PMCID: 3184995
PMID: 21991310
DOI: 10.1371/journal.pone.0025369
call_split See protocol

[…] 0.5–0.9 nmol cm−2) using a Hamilton syringe extending beneath the barrier, and the surface pressure π was recorded as a function of time. Adsorption data were analysed with the software SDAR from the PCSB program collection . […]

Citations

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PCSB institution(s)
Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD, USA

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