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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.
The PCSB Matrix and Vector classes are partially based on the JAMA code (Hicklin et al., 1999).
Please note: We strongly 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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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 v2.8; Manual |
| 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 |
| 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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Differential scanning fluorimetry melting data analysis.
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DMAN is a program to analyse protein thermal denaturation data obtained by multi-well differential scanning fluorimetry. Experimental repetition schemes on multi-well plates can be defined using an ASCII file or through a graphical user interface (GUI). The raw or pre-processed protein denaturation data are read by DMAN, and results of replica wells are averaged with the mean melting temperature and the estimate of standard deviation being calculated. Based on a z-test, outliers are automatically excluded. The results are annotated to highlight wells that show a significant difference in melting temperature from a reference well, as well as the level of significance determined by a t-test.
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| Download: DMAN v1.5; Manual |
| When using this program, please cite: |
Wang, C.K., Weeratunga, S.K., Pacheco, C.M., Hofmann, A. (2012)
DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments.
Bioinformatics 28, 439-440.
DOI | PubMed | 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 |
| 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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SBAL is a program for multiple protein sequence alignments guided by secondary structure elements. The program provides automatic and semi-automatic alignment features, and also possesses manual editing capabilities.
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| Download: SBAL v1.0; Manual |
| 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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SDAR (Serial Data Analysis and Regression) is a Java application for graphical analysis, transformation and fitting of serial data.
Numeric data in the form of multi-column ASCII files can be read into the program and graphed as x-y-plots. Images can be saved in SVG, PNG or TIFF format.
This application makes use of select parts of Michael Flanagan's Java library (Flanagan, 2010).
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| Download: SDAR v1.9 |
| 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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Flanagan, M. T. (2010)
Michael Thomas Flanagan's Java Scientific and Numerical Library.
http://www.ee.ucl.ac.uk/~mflanaga/java/
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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 | Wang, C.K., Weeratunga, S.K., Pacheco, C.M., Hofmann, A. (2012)
DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments.
Bioinformatics 28, 439-440.
DOI | PubMed | More |
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