There are many biological problems which can be approached with Rosetta. These topics often stem from the central idea that sequence confers structure which in turn confers function. For example, Rosetta was initially utilized for de novo protein structure prediction (sequence->structure), while current applications can be as extensive as enzyme design (function->sequence).
Generally speaking (for most biological problems), the computational challenges faced are two-fold. First, can we adequately sample the space where the solution to our problem lives? Second, can we identify said solution, if we have sampled it? This should be kept in mind when deciding on which protocol to apply to your problem, how many models to generate, and which score function to use.
If this page doesn't have a problem that sounds like yours, it may be that you haven't determined what the problem is, or that we can't solve it. If you are thinking of your problem from an angle of sampling a specific degree of freedom, see this page.
The general question to be answered below: given a sequence, can I predict the protein structure? There are two approaches to predicting protein structure from sequence alone: de novo and comparative or homology modeling. There are also other, more specialized, approaches for particular tasks such as antibody homology modeling, symmetric homooligomer modeling, and membrane protein modeling.
De novo structure prediction is useful when modeling a protein with low homology. In the de novo algorithm, the protein sequence is initiated in an extended conformation and "folded" by changes in phi/psi angles sampled from n-mer fragment libraries. De novo structure prediction is accurate when modeling a small (<100 residues), globular protein.
See: Ab initio Modeling Tutorial, Tutorial on protein folding using the Broker and Ab initio.
Comparative modeling on the other hand tends to be successful when the target sequence (sequence of interest) has a high degree of sequence homology (>50%) with a protein whose structure has been determined. Typically, the protein sequence of interest is threaded on to the determined structure and the areas of low homology are modeled by loop closure (see below) or another technique.
See: Comparative Modeling Tutorial, Comparative Modeling (potentially out of date) and Comparative Modeling via RosettaScripts (uses RosettaScripts) for more information.
Another general question which can be interrogated by Rosetta is: given protein A and protein B, can I generate a plausible model for protein–protein interactions? This problem can be conflated with the protein structure prediction problem when the structure of either protein A, protein B, or both are unknown. Protein flexibility can play a role in protein docking by increasing the degrees of freedom. For example, high RMSD between the bound and unbound states makes prediction of the bound state from the unbound states difficult. On the other hand, biochemical information can be implemented as constraints (see below) in the scoring function during docking to (hopefully) improve model accuracy.
In general, there are three types of docking: global, local, and local refine. These are all run via the docking protocol, but differ in flags. Check out this introductory tutorial on protein-protein docking.
Global docking entails a random initial placement of both partners, a low-resolution centroid phase with (relatively) large rigid-body translations, and a high-resolution, full-atom phase with smaller perturbations and side-chain repacking/minimization.
Local docking is identical to global docking except the initial placement of the partners is not random thereby ensuring that interactions are sampled about the initial configuration.
Local refinement docking only uses the high-resolution, full-atom phase.
See the docking protocol for more information on how to run a docking simulation. Note: side-chains should be pre-packed prior to docking to globally minimize side-chain energies since docking only packs side-chains at the interface.
In this case, (near) atomic-resolution structures have been determined for both interacting partners. The structures should be prepared for docking in the standard manner (see preparing structures, pre-packed). The docking protocol would then search for the complex structure with minimal energy.
Docking can emulate several biophysical models of protein–protein interactions which are enumerated below.
The lock and key model assumes that proteins interact in a rigid fashion; two proteins must have shape complementarity to interact. Assuming the two protein partners are not expected to have backbone motions upon binding, the problem can be approached with rigid-backbone docking.
Under the conformer selection model, proteins are viewed as a statistical ensemble of conformations including the bound and unbound conformations of each partner. For the bound complex to form, the bound conformations of each partner must encounter each other. To computationally model this behaviour, an ensemble of structures can be generated for that partner (or both) using the relax protocol. To be useful for docking, an ensemble of structure should not deviate further than one Angstrom RMSD from the initial model. These ensembles of structures can be sampled during the docking protocol.
The induced fit model offers an alternative to the prior two models.
Induced fit holds that upon an encounter, proteins mutually affect each other.
This is computationally modeled by minimizing backbone degrees of freedom (in addition to the typical minimization of side-chain degrees of freedom) in the high-resolution phase of the docking protocol.
As of June 9th, 2015, there is a -bb_min_res flag which can be used to specify residues with backbone degrees of freedom during minimization, but backbone minimization during docking has not been thoroughly tested.
This is simply a combination of the prior two models. Computationally, an ensemble of structures and backbone minimization are both implemented.
This problem is slightly more complicated and more difficult. Results are less accurate due to the added necessity of homology or de novo modeling one protein. The best approach is to input an ensemble of models for the protein of unknown structure. There is a caveat as ensemble docking swap models according to the Metropolis criterion and so the ensemble cannot have too much diversity or else it will be utterly useless.
Plausible, but this is not recommended. Success would be extremely unlikely due to the large amount of sampling needed to (A) accurately model one partner, (B) accurately model the other partner, and (C) accurately model the interaction between the two partners.
Symmetric Docking is useful for assembling multiple subunits according to a specific symmetry defined in a symmetry file.
Protein–peptide docking is useful for determining the structure of a short, flexible peptide in the context of a receptor. Rosetta has protein–peptide docking methods that work best starting from an approximate model with a starting position near to the peptide–binding site; within five Angstroms backbone RMSD is ideal. Thus, it is not generally tractable to concurrently sample peptide conformations and all the possible binding sites on the surface of the protein. Rosetta also has the capacity to sample conformations of peptidomimetic molecules, such as oligooxopiperazines, hydrogen bond surrogate helices, stapled peptides, peptoids, beta peptides, and more.
Can I predict how a small molecule will interact with my protein? As with protein–protein docking, the better your initial structures are, the more likely you are to produce an accurate model (see above). RosettaLigand or RosettaLigand via RosettaScripts can be used to predict protein–ligand interactions. RosettaLigand run via the executable (is currently outdated). It is preferred to dock ligands via RosettaScripts. An alternative method, is to use Docking Approach using Ray Casting (DARC). Unlike RosettaLigand, which explores protein–ligand interactions in a biological manner via translations and rotations (correct me if this is wrong), DARC evaluates the shape complementarity of a ligand for a pocket on the protein surface.
While protein structure prediction seeks to identify low energy structures in space, protein design seeks to identify amino acid identities in sequence space. Protein design can be used to study both how sequence confers structure (i.e. predicting the amino acid sequence of a given fold) or how structure confers function (i.e. predicting the amino acid sequence for a given function). Due to the breadth of these challenges, protocols are either specific or custom generated using one of the Rosetta scripting interfaces. Broadly, protein design can be performed with the use of a resfiles and flags whenever sidechains are repacked.
One could envision a simple design problem where they seek to stabilize a known protein structure. A reasonable assumption to make is that there will not be large changes in protein fold. Hence, this problem is approached with fixed backbone design where side-chain amino acid identities are sampled to identify those which minimize energy on the current backbone. Further, if design is yield an amino acid sequence favoring hydrophobic residues then fixed backbone design can be run with consideration of hydrophobic surface patches. However, new score functions have limited this problem.
Other design problems of interest may include:
Anchored Design Peptide Design
Loop modeling is a complex and central element of protein structure prediction and design. There are two typical biological problems:
For explicit refinement of crystallography data, see here.
loops from density is a script to take badly fit electron data and a cutoff suggesting how much of the pose you're willing to rebuild and to generate input "loops" files for loop modeling.
For modeling of missing loops on existent protein structures, you can use any of the methods in the section below.
What if I am building a homology model and there are regions with low homology or no predicted secondary structure? These are the typical problems solved by loop modeling algorithms. Most loop modeling algorithms in Rosetta are contained within a single executable and run by setting different flags. The fastest, but least accurate method is cyclic coordinate descent (CCD). CCD closes a loop by iteratively solving for phi/psi angles which position the mobile terminus closer to the target anchor after fragment insertion. CCD is generally not recommended but can be used in specific cases (e.g. when time is a limiting factor). The currently (June 10th, 2015) accepted method of loop modeling is next-generation KIC (NGK). KIC sampling can be enhanced/concerted with fragments (KIC with fragments). There also exists an alternative, Monte Carlo stepwise, loop modeling method which can be applied to proteins and RNA. Unfortunately, stepwise loop modeling (for proteins and RNA) tends to be slow.
See the Kortemme Lab benchmark server for a comparison.
You probably should not be doing this using Rosetta, if at all. Disordered proteins are dynamic in the context of a cell. It is unlikely that any static, in silico, model of a disordered protein or protein region will be very accurate. Rosetta's scorefunctions are parameterized on crystallized proteins, not disordered proteins. However, if you have a specific question, such as "can my disordered tail of 20 residues plausibly interact with this other region of my protein?" Then you may begin to approach this question with FloppyTail.
For explicit refinement of crystallography data, see here.
mr_protocols is typically used alongside Phaser / PHENIX; it uses Rosetta's comparative modeling to rebuild gaps and insertions in the template, as well as missing density, from fragments, followed by relaxation with constraints to experimental density. You can then use Phaser / PHENIX again to re-score against crystallographic data.
ERRASER refines RNA structures from electron density (crystallographic data); it constitutes a workflow of erraser_minimize, swa_rna_analytical_closure, and _swa_rna_main. It requires the use of the refinement program PHENIX.
It may be that your question cannot be answered. Or, perhaps you can construct a protocol out of RosettaScripts or PyRosetta. See this page for more details.