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Introduction
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The Programme Collection for Structural Biology and Biophysical Chemistry (PCSB)
comprises several Java applications for recurring tasks in the area of structural
biology and related disciplines.
We recommend using Sun Java.
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The applications are available for academic usage free of charge.
Please report any problems (email).
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To download the
software, right-click on the application and Save Link As a .jar file. Do not un-zip
the downloaded file.
Internet Explorer: When pointing at the download link, the info may say '{application-name}.jar', but upon
downloading the file might be saved as '{application-name}.zip'. The downloaded file needs to be re-named
to '{application-name}.jar'.
A Manual and Reference PDF file is included in most applications, but also available as direct download.
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Running the software under Windows
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To run the software, simply double-click the .jar file.
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Running the software under Linux
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Depending on your Java installation, the applications might run by typing
java -jar {application-name}.jar
Alternatively, you might want to use a shell script, e.g.:
#!/bin/csh -f
setenv JAVA {path-to-java-bin-directory}/java
setenv CLASSPATH {path-to-pcsb-application-file}/{application-name}.jar
$JAVA {application-name} $*
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Automated circular dichroism data processing.
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ACDP is a Java application for processing protein circular dichroism (CD) spectra either individually or within a series. Data processing includes spectrum subtraction ('baseline correction'), conversion of the raw CD into units of mean residue ellipticity, wavelength monitoring and graphical inspection. Three different algorithms for secondary structure deconvolution have been implemented, and spectra can be analysed without the need for data reformatting using a neural network approach, variable selection or linear combination of prototype spectra.
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This program requires JRE 1.6 or higher.
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| Download: ACDP v2.6b; Manual, References |
| When using this program, please cite: |
Hofmann, A. (2009)
ACDP - a Java application for data processing and analysis of protein circular dichroism spectra.
J. Appl. Crystallogr. 42, 137-139.
DOI | More | |
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Automated fluorescence data processing.
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AFDP is intended for processing and analysis
of a series of fluorescence spectra recorded within a serial experiment like, for example, unfolding or
titration series. The main idea of the programme is to enable quick baseline correction and extraction of peak wavelength and intesity data
using a set of data files containing sample and baseline fluorescence data.
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| Download: AFDP v2.4a; Manual, References |
| When using this program, please cite: |
Hofmann, A., Wlodawer, A. (2002)
PCSB - a programme collection for structural biology and biophysical chemistry.
Bioinformatics 18, 209-210.
PubMed | PDF | More | |
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Peptides is a program for calculation of peptide/protein parameters from a given sequence. It calculates number
of residues, molecular mass, the molecular formula, volume, pI, amino acid content and a pH-charge correlation
('titration curve').
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| Download: Peptides v2.5; Manual, References |
| When using this program, please cite: |
Hofmann, A., Wlodawer, A. (2002)
PCSB - a programme collection for structural biology and biophysical chemistry.
Bioinformatics 18, 209-210.
PubMed | PDF | More | |
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Serial data arithmetic and curve fitting.
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Images can be saved in Postscript, PNG or TIFF format. For the PNG and TIFF option, this program
requires installation of the
Java Advanced Imaging Image I/O Tools.
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| Download: SDAR v1.5 |
| When using this program, please cite: |
Hofmann, A., Wlodawer, A. (2002)
PCSB - a programme collection for structural biology and biophysical chemistry.
Bioinformatics 18, 209-210.
PubMed | PDF | More | |
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X-ray crystallographic data lookup.
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This application provides a lookup of anomalous scattering coefficients, symmetry operators
(in various different formats), the calculation of symmetry-related points for a given
spacegroup, and calculation of the Matthews parameter.
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| Download: Tables v1.6 |
| When using this program, please cite: |
Hofmann, A., Wlodawer, A. (2002)
PCSB - a programme collection for structural biology and biophysical chemistry.
Bioinformatics 18, 209-210.
PubMed | PDF | More | |
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Hicklin, J., Moler, C., Webb, P., Boisvert, R.F., Miller, B., Pozo, R. & Remington, K. (1999)
JAMA : A Java Matrix Package.
http://math.nist.gov/javanumerics/jama/
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Hofmann, A. (2009)
ACDP - a Java application for data processing and analysis of protein circular dichroism spectra.
J. Appl. Crystallogr. 42, 137-139.
DOI | More | Hofmann, A., Wlodawer, A. (2002)
PCSB - a programme collection for structural biology and biophysical chemistry.
Bioinformatics 18, 209-210.
PubMed | PDF | More | Hu, N.-J., Currid, M., Daley, M., Hofmann, A. (2005)
Two new software applications for automated processing of circular dichroism and fluorescence data.
Appl. Spectrosc. 59, 68A.
Publisher | More |
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