Applications: 4 applications/pipelines from the larger CCP4 suite: Balbes, MrBUMP, Zanuda, jsPISA. Soon to be added, 3 more pipelines: Ample, Shelx and Crank2.
The Protein Crystallisation Construct Designer (ProteinCCD) is a tool to help deciding how to choose promising constructs for protein expression and crystallisation. A specific feature of CCD is that since it starts from the DNA sequence, it keeps track of the protein-DNA relationship. Thus, although all the analysis and construct choice is being done in the protein level, CCD can be used to suggest primers for PCR amplification of the chosen constructs, since it also knows the DNA sequence.
The PDB_REDO server is a tool for macromolecular X-ray crystallographers who wish to optimize the refinement of their structure. It takes as input the coordinates of a macromolecular structure you are working on (PDB file), together with the associated X-ray diffraction data (MTZ file), and returns a refined and partially rebuilt model and a validation report.
Information driven biomolecular docking based on the HADDOCK software as described in http://www.bonvinlab.org/software/haddock2.2Several access levels to the portal are provided exposing an increasing number of options / parameters:
- HADDOCK server: the Easy interface
- HADDOCK server: the Prediction interface
- HADDOCK server: the Expert interface (requires Expert level access)
- HADDOCK server: the Refinement interface (requires Expert level access)
- HADDOCK server: the Guru interface (requires Guru level access)
- HADDOCK server: the Multi-body interface (requires Guru level access)
- HADDOCK server: the File upload interface
- HADDOCK server tool: generate AIR files for multibody docking
Subset of workflows implemented in Scipion and accessed through a webpage. These tools provides a good way to try the different processing workflows without any local installation.
3DBIONOTES-WS is a web application designed to automatically annotate biochemical and biomedical information onto structural models. Current sources of information include post-translational modifications, genomic variations associated to diseases, short linear motifs, immune epitopes sites, disordered regions and domain families.
Chemical-shift based NMR structure calculations using rosetta.
Molecular dynamics (MD) simulations on biological systems with AMBER, in particular (but not only) using NMR-derived information as restraints for MD.