Rosetta 3.2 Release Manual

How to prepare structures for use in Rosetta

Author:
Coallated by Steven Lewis and Ramesh Jha

Purpose

Structures derived straight from the PDB are not always perfectly compatible with Rosetta - it is common for them to have clashes (atom overlaps) or other minor errors. It is often beneficial to prepare the structures before doing real work on them to get these errors out of the way beforehand. This provides several benefits:

How do I prepare structures?

How to prepare your structures is unfortunately closely linked to what you want to do with them. In other words, your main protocol dictates your preparation protocol. Remember that all you're really doing here is relaxing into Rosetta's energy function - you're not necessarily making it objectively more correct (although clashes are generally wrong), you're really just making Rosetta like it better. What follows is advice from many of the Rosetta developers on how to best prepare structures.

Original question from Ramesh Jha

Is there a consensus protocol to create the starting PDBs to be used in mini? It is not unknown that the PDBs right from the Protein Data Bank are composed of artifacts and defects that can give an exceptional jump in energy if happened to be altered during a design protocol. In order to minimize this problem, there are a few things which can be tried and that I am aware of: Having tried all of them, I thought the option 3, was the best one, where I used fast relax while using -use_input_sc flag. But recently I observed that though 'relax' is able to substantially decrease the energy of starting PDBs, also result in subtle movements in the backbones and a PDB which could accommodate a ligand could not anymore after being relaxed.

James's reply

Try adding the -constrain_relax_to_start_coords option to your protocol #3.

Ben's reply

I've been using a protocol that does sc & bb minimization, full packing with -use_input_sc, then minimization of bb, rb, and sc. It's located in: src/apps/pilot/stranges/InterfaceStructMaker.cc The idea with this is that it keeps things from moving too far from the starting structure. There's no backbone sampling so I typically find rmsd to the xtal structure to be < 1.0. Relax actually will do explicit bb sampling thus gives a lower energy structure than my protocol but can also introduce the changes that you observed. I'm pasting my typical options file below:
-database /Users/stranges/rosetta/minirosetta_database
-nstruct 20
-ndruns 10
-no_his_his_pairE
-run::min_type dfpmin_armijo_nonmonotone
-ignore_unrecognized_res
-use_input_sc
-ex1
-ex2
-no_optH false
-overwrite
-allow_rbmin true
-min_all_jumps true
-mute protocols.moves.RigidBodyMover protocols.moves.RigidBodyMover core.scoring.etable core.pack.task protocols.docking.DockingInitialPerturbation protocols.TrialMover core.io.database

Sagar's reply

I just use repack with sc_min, and include the ligand in the process.

Rocco's reply

There is a fixed-backbone minimization program that's part of the ligand docking application, ligand_rpkmin (See section "Preparing the protein receptor for docking" of http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_ligand_docking.html).

It won't relieve any backbone strain, though, so you may still have issues if the downstream protocol allows for backbone movement.

Steven C.'s reply

In general, the Meiler lab does the following: This will alleviate clashes in the protein and give a good starting structure for any of the Rosetta applications...unless the protein blows up for some reason.

With an addendum from James Thompson: Thanks Steven! That's a very reasonable way to gently structures from the PDB, although there are a lot of different ways that you might try this.

Here are two more things that come to mind:

With a second addendum from Andrew Leaver-Fay: I thought I might point out two things:

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