How to submit a job to RBO Aleph?
What does RBO Aleph output as result for my query sequence?
How are my uploaded contact restraints integrated into the prediction pipeline?
Can I switch off the usage of server predicted contacts completely?
Can I upload distance restraints from e.g. cross-linking experiments or other sparse experimental data?
How long does a modeling run take for my protein?
How much does the prediction runtime increase when domain splitting and assembly are used?
What is EPC-Map?
What is MBS?
How to submit a job to RBO Aleph?
- Go to the page “Submit job“.
- Enter your query sequence into the text field named “Sequence (FASTA)”. You find a detailed explanation of the required format of the input sequence here.
- (Optional) Upload your own contact restraints file to guide RBO Aleph’s ab initio modeling. You find a detailed explanation of the required format of the contact restraints file here, and how the contacts are integrated into the pipeline here.
- Enter the job name into the text field named “Jobname”.
- (Optional) If you enter your email address in the text field named “E-Mail” you will get an email with the link to the future results page for your prediction. You will automatically receive a notification when the job is finished. In case no email is given the server shows the link to this future results page in the current browser window after you submitted the job. You may store the link as a bookmark to visit the page again when the job is finished. The typical runtime of a job will be several hours depending on the length of the target.
- (Optional) Select the type of modeling RBO Aleph should perform. The default modeling protocol is automatic. In this case, RBO Aleph automatically decides whether to use template-based or template-free ab initio modeling depending on the presence of a suitable target. You may “override” this automatism by actively selecting “Template-based modeling” or “Ab initio” instead. Then RBO Aleph will only run the chosen protocol.
- RBO Aleph automatically runs domain boundary prediction if the input sequence is longer than 250 residues. When “Automatic” modeling is selected you may deactivate the domain splitting process by deselecting domain splitting.
- Click on “Submit job” when you are done with entering the required input.
What does RBO Aleph output as result for my query sequence?
RBO Aleph presents the prediction results on a separate web page accessible only to the job submitter. It is divided into five parts (see Sample results):
- General information about the job, detected domains (color-coded), the modeling method used for each domain, and a list of used templates.
- Interactive contact and 3D structure visualization of the five best predicted models with the following features:
- easy inspection of other models via drop down menu, where the initially loaded model refers to the best prediction,
- visualization of the predicted contacts as dashed lines, top scoring L/10 contacts are initially shown where L refers to the length of the protein sequence (1.5L contacts were used to guide ab initio prediction),
- different coloring schemes by: sequence position, predicted error (red refers to high error and blue to low), domain, or secondary structure type,
- ability to hide viewer menu at the right to increase size of 3D canvas, e.g. for stereo view or larger proteins.
- 2D plot of local prediction error estimate over the whole protein length, coloring is the same as for the 3d model when display mode by predicted error is active.
- Contact map visualization of predicted contacts, same top scoring L/10 contacts are initially shown (selection of other subsets via drop down menu of the 3D viewer)
- Download section that contains download links for the predicted models and contacts (in CASP11 format) separately, as well as a ZIP-archive that additionally contains the template alignment (in FASTA format) if templates were used.
How are my uploaded contact restraints integrated into the prediction pipeline?
RBO Aleph uses the accepted contact restraints to guide ab initio modeling as follows: The server linearly combines user defined contacts with its own predicted contacts by EPC-map. Currently, both contact lists have equal weight in the linear combination.
Can I switch off the usage of server predicted contacts completely?
Leveraging contact information to guide protein structure prediction is one of the key features of RBO Aleph. We integrate this information at several points in our pipeline. Therefore, you cannot switch off the server predicted contacts completely when using our fully automated server. However, we will consider to allow users to modify the weighting factor of the uploaded contacts in a future version of RBO Aleph.
Please contact us if you want to run plain ab initio modeling with model-based search (MBS) without using the predicted contacts from EPC-map.
Can I upload distance restraints from e.g. cross-linking experiments or other sparse experimental data?
Currently, RBO Aleph only accepts residue-residue contact restraints of 8 Ångstrøm distance. We are working on an updated version of RBO Aleph to automatically integrate distance restraints from cross-linking (CASP Tx experiments) or other sparse experimental data into the structure prediction pipeline.
Please contact us if you want to use your own cross-linking restraints to guide ab initio modeling with model-based search (MBS).
How long does a modeling run take for your protein?
The runtime of a prediction usually depends on the length and difficulty of the target sequence, whether domain splitting is used or not, and the workload of our server. The runtime may be:
- ~ 4 hours up to several hours for easy targets
- ~ 1 day up to several days for difficult targets
Practically, the duration of the prediction also depends on the number of jobs running in parallel on the server. On average, our server is able to process up to five simultaneous template-based modeling predictions and one ab initio prediction.
Please contact us if your job has not been finished within 72 hours.
How much does the prediction runtime increase when domain splitting and assembly are used?
Domain assembly is only used when RBO Aleph detects a suitable domain boundary either based on template- or sequence-based domain prediction. In such a case the structure of each domain will be predicted separately. Afterwards, RBO Aleph uses a domain assembly protocol to join the individual domains into one continuous structural model. Especially this assembly process may increase the runtime by several hours up to days depending on the number of domains.
What is EPC-Map?
EPC-Map stands for using “Evolutionary and Physicochemical information to predict Contact maps“. To determine accurate contact information for a wide range of proteins, EPC-Map leverages two complementary sources of information: evolutionary and physicochemical information. Evolutionary information contained in multiple-sequence alignments identifies residue pairs that are close in space, which co-evolve to maintain structural stability, with a global statistical model. Physicochemical information identifies native contacts contained in predicted low-energy decoys by evaluating each contact’s local physicochemical environment using a novel graph-based representation. Please refer to our original publication for detailed information.
What is MBS?
MBS stands for “Model-Based Search”. MBS is a highly effective conformational search strategy that extracts relevant information from observations made during search to use it as further guidance. Model-based search identifies funnels in the energy landscape using an all-atom energy function and incrementally increases the focus on regions in the conformational space that are most likely to contain the native structure. Please refer to our original publications for detailed information.