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PCSB: Programme Collection for Structural Biology and Biophysical Chemistry | Update: 2002-10-03 |
| Structural characterisation of proteins very often involves more than structure determination by X-ray crystallography or NMR techniques. Such different phenomena as, for example, domain motions, ligand-binding, or folding stability are also commonly investigated in structural laboratories. This involves series of spectroscopic experiments that always require the recording of “baseline spectra” as controls, thus increasing the amount of data to be processed. In subsequent analyses, sample spectra have to be corrected against their respective controls and very often the conversion of raw data is necessary as well (for example, for CD data). Additionally, crystallographic problems frequently require the alignment of proteins or the knowledge of certain parameters such like anomalous scattering factors, solvent content, or symmetry operators. A convenient lookup of these data on the available computer system is another task addressed here. |
| At the same time, modern structural laboratories utilise multiple computing environments ranging from personal and bench-top computers based on WINDOWS, LINUX or MAC-OS operating systems to supercomputer clusters that are run under UNIX. Furthermore, graphical user interfaces are powerful features in versatile computer programs due to the ease of handling and being self-explanatory in many applications. |
| The immense popularity of the Java programming language (Sun Microsystems), the obvious advantage of the ability of Java applications to run under virtually any operating system, and the easy generation of graphical interfaces provides the ideal background to set up a compilation of utility programs with graphical user interfaces intended to simplify a variety of tasks of structural laboratories. |
| PCSB has two aspects: |
| To exploit the entire potential of Java we generated fundamental classes (similar to the Java Foundation Classes), which enable the handling of objects within structural biology and biophysics. These classes are to simplify algorithm construction for our applications and can also be employed by other groups designing their own programs. |
| The second aspect deals with the applications themselves where a user-friendly design and specific “structural” questions are addressed. |
| These PCSB foundation classes are currently available: | |
| PCSB.AASequence | Amino acid sequence handling and representation. |
| PCSB.EigenvalueDecomposition | Eigenvalues and eigenvectors of a real matrix. This class has been imported unchanged from Hicklin et al. (1999). |
| PCSB.Matrix | Matrix operations. |
| PCSB.PDBfile | Coordinate handling and transformation, operations within PDB files. |
| PCSB.SymLib | Setup of crystallographic symmetry classes. |
| PCSB.Utility |
Convert FixWidth LinePrinter MLib Snap StatusBar Utility operations and tools. |
| PCSB.Vector | Vector operations. |
| The current release of PCSB comprises the following programs (applications): | |
| PCSB (v2.1) | |
| Biochemistry | |
| Peptides | Peptide parameter calculation |
| Biophysics | |
| ACDP | Automated CD Data Processing |
| AFDP | Automated Fluorescence Data Processing |
| Crystallography | |
| Align | Alignment of three-dimensional structures |
| Symmetry | Calculation of rotation axes |
| Tables | Lookup of anomalous scattering factors, symmetry operations and calculation of the Matthews coefficient |
| Screenshots from ALIGN: | |||
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| Documentation is available as a PDF file. |
| The PCSB applications and foundation classes are available free of charge. If you are interested in PCSB, please send an email. |
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/ |
Hofmann, A. & Wlodawer, A. (2002) PCSB - A Program Collection for Structural Biology and Biophysical Chemistry. Bioinformatics, 18, 209-210. PubMed | PDF | PDF (Journal) |
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