NPDock predicts complexes of protein-nucleic acid structures which implements a computational workflow that includes docking, scoring of poses, clustering of the best-scored models and refinement of the most promising solutions.
Currently npdock seems to be offline, hope that is just a temp issue with the server.. Basically you need to enter to the interface the PDB ID (3D structure prediction file) for the protein you would like to try and dock the nucleic acid and the PDB ID of that RNA/DNA molecule - npdock will next try to predict the optimal docking positions of the two and display the results
You may learn more in the original publication: https://academic.oup.com/nar/article/43/W1/W425/2467938/NPDock-a-web-server-for-protein-nucleic-acid
0 upvotesReply
Posted: 2 years ago
Zeshan Haider
Bioinformatician at Government College University, Faisalabad
Bioinformatician at Government College University, Faisalabad
but now np dock website is offline ,,but i want to urgent to work on it,when its website will open? and anyone now as another software for protein to dna docking? suggesst me
You may also use @patchdock for this purpose.. We have contracted the creators of NPDock and they assured us they are informed of the situation with their server and are working to get it up-and-running soon
0 upvotesReply
Posted: 2 years ago
Zeshan Haider
Bioinformatician at Government College University, Faisalabad
Zeshan Haider
Bioinformatician at Government College University, Faisalabadhelp
how can i use npdock ?
Roy Granit
Co-founder at LabWormCurrently npdock seems to be offline, hope that is just a temp issue with the server.. Basically you need to enter to the interface the PDB ID (3D structure prediction file) for the protein you would like to try and dock the nucleic acid and the PDB ID of that RNA/DNA molecule - npdock will next try to predict the optimal docking positions of the two and display the results
Zeshan Haider
Bioinformatician at Government College University, Faisalabadbut now np dock website is offline ,,but i want to urgent to work on it,when its website will open? and anyone now as another software for protein to dna docking? suggesst me
Roy Granit
Co-founder at LabWormYou may also use @patchdock for this purpose.. We have contracted the creators of NPDock and they assured us they are informed of the situation with their server and are working to get it up-and-running soon
Zeshan Haider
Bioinformatician at Government College University, Faisalabadpatch dock can use for proteien to dna docking