NPDock

Load example:
The exemplary output with explanations for the demo input can be found here.

Submit

Dear Users, because of a huge number of jobs submitted to the NPDock server, we have to change the limit of submitted jobs to 1 per user. Sorry for any inconvenience!

Please run max. 1 jobs at the same time. If you need to run more jobs, please consider installing NPDock (DARS-RNP) locally. Sorry for any inconvenience!

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Docking
Complex Refinement

RNA-protein DNA-protein Protein:

Select file Change Remove

RNA/DNA:

Select file Change Remove

RNA protein - demo loaded! demo/rna.pdb demo/protein.pdb

DNA protein - demo loaded! demo/dna.pdb demo/1VHI.pdb

Select chains:

e.g. A,B,C or `*` to select all chains

e.g. D,E,F or `*` to select all chains

Optional parameters:

Number of decoys to be generated with GRAMM

max is 50000, the more decoys are generated, the slowest is the simulation

Interfaces filtering:

Protein interface:	e.g. 161:A or 10-33:A,5:B,18:B or `*` potential interface residues
RNA/DNA interface:	e.g. 161:A or 10-33:A,5:B,18:B or `*` potential interface residues
Number residues of interfaces in contact:

Advanced optional parameters:

Clustering procedure:

Number of the best scored models used for clustering:	less than 1000 is recommended
RMSD cut-off for clustering [Ångström]:	less than 10 is recommended

RNA-protein complex DNA-protein complex

Select file Change Remove

Refinement with MC:

Number of steps of simulation:
Temperature of the first step of simulation [in Kelvin]:
Temperature of the last step of simulation [in Kelvin]:

Every accepted step is saved Lowest energy structure is saved every step