Hofmann Laboratory

The Program Collection for Structural Biology and Biophysical Chemistry (PCSB) comprises several Java applications for recurring tasks in the area of structural biology and related disciplines. At the core of all PCSB applications are the PCSB foundation classes that provide numerical algorithms, classes for handling structural objects, as well as visualisation.

The PCSB Matrix and Vector classes are partially based on the JAMA code (Hicklin et al., 1999). The PCSB LinearRegression, NelderMead and TTest classes use select parts of Michael Flanagan's Java library (Flanagan, 2010). The PCSB LevenbergMarquardt class is based on the class LM by J P Lewis. Some PCSB applications use classes provided by the Apache XML Graphics Project, the W3C Document Object Model, iText PDF libraries, and the BarChartCellRenderer by Thierry Lafont.

The PCSB applications have been developed using Sun/Oracle Java.

Most of our software is distributed under the GNU Affero General Public License.
Please report any problems (email).

To run the stand-alone Java applications, simply double-click the .jar file.

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} $*

Automated circular dichroism data processing.

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.

Download:

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.

Automated fluorescence data processing.

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 intensity data using a set of data files containing sample and baseline fluorescence data.

Download:

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.

Analysis of secondary structure elements in proteins.

ASSP is a Java application for analysis of secondary structure of three-dimensional protein models. It is based on the algorithm used in DSSP (Kabsch & Sander, 1983). A user-supplied structure in form of a PDB file will be analysed for H-bonding and geometric parameters to deliver a secondary structure assignment.

Download:

When using this program, please cite:

Wang, C.K., Hofmann, A. (2015) An integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements. 3Biotech 5, 87-92.

Compound appraisal (cApp home page).

cApp is a Java application that aids handling and storage of information about small-molecule compounds. With the application, the user can appraise compounds with respect to their physico-chemical properties and present structural information together with calculated or measured properties. Structures can be provided by the user in the form of SMILES^TM, InChI, structure-data files (SDF) or added via the embedded chemical editor.
This software makes use of the CDK and SMSD.

Download:

Amani, P., Sneyd, T., Preston, S., Young, N.D., Mason, L., Bailey, U.-M., Baell, J., Camp, D., Gasser, R.B., Gorse, A.-D., Taylor, P., Hofmann, A. (2015) A practical tool for small-molecule compound appraisal. J. Cheminformatics 7, 28.

Externally reviewed by: Macs in Chemistry

Chemical drawing software (cDraw home page).

The Java desktop application cDraw is an interactive chemical drawing software for generation of publication-quality figures. The user interface has been designed with a clear focus on intuitive and convenient handling. The drawings generated in cDraw can be exported as EPS, PDF, PNG, SVG or TIF images. The main file format used to store cDraw drawings builds on CDML, an XML-based format developed for BKChem; however, cDraw also has basic import/export capability for CDXML, CML and SDF file formats.

Download:

Hofmann, A., Coster, M.J., Taylor, P. (2019) Disseminating a free, practical Java tool to interactively generate and edit 2D chemical structures. J. Chem. Educ. 96, 1262-1267.

Differential scanning fluorimetry melting data analysis (DMAN home page).

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. Outliers in a set of replica are automatically excluded based on Grubbs' test using a probability threshold of 95%. The results are annotated to highlight wells that show a significant difference in melting temperature from a reference well, as well as the p-value for this difference determined by Welch's t-test. The melting curves and the location of determined inflection points can be graphically displayed for each set of replica; the user can also determine the inflection point interactively.

Download:

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.

Multi-well plate analysis (DRfit home page).

DRfit is a Java tool for analysis of multiple data sets comprising replicates of discrete bivariate data. In particular, the software has been designed to allow convenient analysis of data structures obtained from multi-well plate assays.

Download:

Hofmann, A., Preston, S., Cross, M., Dilrukshi Herath, H.M.P., Simon, A., Gasser, R.B. (2019) DRfit: a Java tool for the analysis of discrete data from multi-well plate assays. BMC Bioinformatics 20, 262.

Bargraph plotting (jBar home page).

jBar is a Java GUI that allows the user to customise a generic script for R that calculates means and standard errors/deviations for numerical replica data collected in dependence of two variables, and presents the results in form of bar plots. A two-sided Student’s t-test is carried out against a user-selected reference and p-values are calculated. The user can enter the data conveniently through the built-in spreadsheet and configure the R pipeline in the GUI. The configured R script is written into a file and then executed. Barplots are generated as PNG, PDF or SVG files and can also be generated as interactive Plotly HTML widgets.

Download:

Hofmann, A., Cross, M., Karow, M.A., Straub, J.H., Clemen, C.S., Eichinger, L. (2019) A convenient tool for bivariate data analysis and bar graph plotting with R. Biochem. Mol. Biol. Edu. 47, 207-210.

Java desktop application application for agglomerative hierarchical clustering.

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Evaluation of solution scattering of biological macromolecules from atomic coordinates.

MolScat is a program to evaluate solution scattering of biological macromolecules from atomic coordinates. The program reads three-dimensional structures provided as PDB files and considers non-water atoms to calculate a scattering intensity curve. If experimental scattering data are provided, MolScat will fit the theoretical scattering curve to the experimental data. Results are provided in form of graphical plots, an ASCII file of the theoretical scattering data (and fit if applicable), as well as goodness of fit and selected biophysical parameters.

Download:

When using this program, please cite:

Hofmann, A., Whitten, A. (2014) Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules. J. Appl. Crystallogr. 47, 810-815.

Java desktop application to query the NCBI nucleotide database and automatically download sequences into a multi-FASTA file.

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Check of amino acid sequence of a protein structure model provided as PDB file.

PdbCompAA is a tool to compare the amino acid sequence of a model supplied as PDB file with that of a reference sequence. The reference amino acid sequence is read from an ASCII file, such as e.g. a file in FASTA format. For all residues in the PDB file, the presence of all required atoms is checked. This software is intended for use in protein structure model building and file validation.

Download:

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.

Peptide and protein physico-chemical properties.

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').

Download:

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.

Small-angle scattering data fitting with rigid bodies (SAFIR home page).

SAFIR is an application to fit small-angle scattering data with rigid body objects, with the main purpose of modelling oligomeric structures of biological macromolecules.
The program allows loading of individual protein monomers or oligomeric structures which can be displayed and oriented as rigid bodies in a molecular graphics viewer. A shape object restored from small-angle scattering data can also be displayed, enabling the user to arrange the protein molecules to fit. For the loaded model, the small-angle scattering can be evaluated and compared to experimental scattering data.
Rigid body refinement of the loaded model has been implemented by means of a Monte-Carlo approach which uses the fit between model-derived and experimental scattering data as target function.

The executable jar file requires Java version 15 or higher.

Download:

Hofmann, A., Whitten, A. (2014) Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules. J. Appl. Crystallogr. 47, 810-815.

Structure-based sequence alignment (SBAL home page).

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.

Download:

When using this program, please cite:

Wang, C.K., Broder, U., Weeratunga, S.K., Gasser, R.B., Loukas, A., Hofmann, A. (2012) SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments. Bioinformatics 28, 1026-1027.

Serial data analysis and regression (SDAR home page).

SDAR 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.

Download:

When using this program, please cite:

Weeratunga, S.K., Hu, N.J., Simon, A., Hofmann, A. (2012) SDAR: a practical tool for graphical analysis of two-dimensional data. BMC Bioinformatics 13, 201.

Pairwise similarities of small-molecule compounds.

Substructure is a tool to calculate pairwise similarities of small-molecule compounds. The program requires two files in structure-data file (SDF) format; one file is the library of target compounds, the other is the library of templates. The template library can consist of one or more than one compounds.
This tool is based on SMSD and also uses parts of the CDK.

Download:

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.

X-ray crystallographic data lookup.

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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When using this program, please cite: