NPDock

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!
In the queue there is/are 70 job(s). It might take up to 230 h to finish.
~3 jobs at the same time, one job ~10h


E-mail address is optional

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
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]:

http://iimcb.genesilico.pl/