You are here

Docking

Docking prepack vs. relax

Category: 
Docking

Is Docking Prepack simply a specialized version of Relax for dealing with complexes? (separate complex, minimize sidechains, reassemble)

If I am docking proteins A and B where each has already been individually relaxed, is there any need for running Docking Prepack on the PDB file that contains both relaxed A and B, already oriented correctly for local docking?

Post Situation: 

Docking membrane ions and water

Category: 
Docking

I'll explain what I do, in case someone has a solution to my problem.
I am trying to perform a docking protein-protein, where, a membrane protein arranged in a lipid membrane and balanced with water and ions, should be bound to a protein.
I need to know how much these structures interfere with docking.


Any tips?

Post Situation: 

Error with non-canonical amino acid in SnugDock.

Category: 
Docking

Hi all,

I'm trying to model the binding of an antibody to a citrullinated peptide. I've created rotlibs and params files for the citrulline amino acid following the protocol in Renfrew, et al. "Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design", doi:10.1371/journal.pone.0032637. Now I'm trying to use SnugDock to model the antibody:antigen binding, but I keep hitting the following error. 

Post Situation: 

Calibur-linux binary or source code availability?

Category: 
Docking

Just wondering if there been any progress toward building the Cailibur program for clustering into RosettaDock?

Is the Calibur source code available anywhere?  All I seem to find is the binary version on the  http://sourceforge.net/projects/calibur/, and I only get this to work on a windows envrionment.  It would be nice to have Calibur version for use on  a Linux platform.

Post Situation: 

General protein-protein docking when no info. on structure is availble

Category: 
Docking

We plan to follow/advise the following steps for protein-protein docking when no known information on the complex structure is available and, it is necessary to do an initial global search around one partner. 

The objective of clustering is to, ideally, seek larger clusters of decoy structures having more closely spaced energies.

Hence, the following sequence of steps is proposed for protein-protein docking where no known information on structure is available:

Post Situation: 

dG_separated threshold for identifying non-binding peptides with InterfaceAnalyzer.

Category: 
Docking
Scoring

Hello,

I am a beginner in protein modelling/analysis and trying to learn through tutorials and the forums here.

A bit of a background of my present Task: I have a crystal structure of an Ab-Ag complex (AbFab with Ag peptide). I also have experimental data on binding affinities of several Ag peptide variants. I want to use this data to predict binding ability of novel Ag peptide variants with the same Ab.

Post Situation: 

Pages

Subscribe to RSS - Docking