The prime purpose of Biskit is to offer you a tool box for creating your own structural bioinformatics programs. In order to make most of this package, you should program your own python scripts around the Biskit library. However, Biskit already contains ready-made programs for several applications -- ranging from a simple script to extract a sequence from a PDB file to a complex workflow for flexible protein-protein docking and a pipeline for automatted homology modelling.
We here give tutorials for some main applications:
- Automatted homology modelling
- Protein-protein docking
- Flexible protein-protein docking
- Structure sampling with Xplor
- Structure sampling with Amber
- Modelling validation
- Electrostatic free energy of binding with DelPhi
You can find the full range of programs in the folder biskit/scripts:
- Grünberg R, Nilges M and Leckner J. (2007) "Biskit - A software platform for structural bioinformatics." Bioinformatics 23(6), 769-70
- Grünberg R, Leckner J and Nilges M. (2004) "Complementarity of structure ensembles in protein-protein binding." Structure 12(12), 2125-36
- Grünberg R, Nilges M and Leckner J. (2006) "Flexibility and conformational entropy in protein-protein binding." Structure 14(4), 683-93
- Charfeddine C, Monastiri K, Mokni M, Laadjimi A, Kaabachi N, Perin O, Nilges M, Kassar S, Keirallah M, Guediche MN, Kamoun MR, Tebib N, Ben Dridi MF, Boubaker S, Ben Osman A, Abdelhak S. (2006) "Clinical and mutational investigations of tyrosinemia type II in Northern Tunisia: identification and structural characterization of two novel TAT mutations." Mol Genet Metab. 88(2), 184-91
- Bouvier, B., R. Grünberg, M. Nilges, and F. Cazals (2009) "Shelling the voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics, and composition." Proteins .
Martel CM, Warrilow AG, Jackson CJ, Mullins JG, Togawa RC, Parker JE, Morris MS, Donnison IS, Kelly DE, Kelly SL. (2010) "Expression, purification and use of the soluble domain of Lactobacillus paracasei beta-fructosidase to optimise production of bioethanol from grass fructans." Bioresour Technol. 101(12):4395-402.
Please quote the Grünberg et al. Bioinformatics paper if you used Biskit for your new publication (and tell us about it :-)) !
Introduction for Biskit developers