RCD+   Fast loop closure modeling

RCD+ server is a fast loop-closure modeling tool based on an improved version of our RCD method [Chys and Chacón (2013)]. Accurate all-atom loop predictions and ensembles can be easily generated in a few minutes for loops of 12 or less residues. Once your job is completed you can interactively check and download the predicted models.

Please, upload a only protein PDB file with the atomic coordinates (or fetch by PDB-ID) and introduce the following parameters: chain id, indices of the start/end residues, sequence, and select the prediction scenario between Native (if the loop environment is reliable) or Modeling (to also include the side-chains of the loop neighborhood in the refinement). The coordinates must avoid any non standard aminoacids/atoms, contain a valid chain id, and include at least the backbone of the two N- and two C-terminal anchor residues (indices Start-2, Start-1, End+1, and End+2). All residues from "Start" to "End" indices (inclusive) will be modeled from scratch.

Test case: Either fetch by ID 2CMD or upload 2cmd.pdb file, and input Chain: A, Start: 270, End: 277, and Sequence: LGKNGVEE.



  




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*If you would like to refer our work use:
Server and improved method López-Blanco JR, Canosa-Valls AJ, Li Y, and Chacón P (2016). RCD+: Fast loop modeling server.
NAR (DOI: 10.1093/nar/gkw395). (Use this reference, please)
Original method Chys P and Chacón P (2013). Random coordinate descent with spinor-matrices and geometric filters for efficient loop closure. J. Chem. Theory Comput. 9:1821-1829.


or select an example

Loop generation stage of RCD+ has been parallelized by MPI. Below, the experimental average time (blue) to generate one 12-residues loop is compared with the theoretical expected time (red) for different number of processing cores in our dual Intel Xeon E5-2650 server (2.00GHz).


*5000 loops were generated using the neighbor-dependent Ramachandran filter and randomly perturbed standard bond angles and lengths with the Park benchmark (Park et al. 2014 PLoS One 9:e113811).

Feel free to explore (or submit again) any of the precomputed examples for the Modeling scenario!


Malate dehydrogenase (2CMD:A, A270-277) (8-residues)
INPUT: ID= 2CMD:A, Chain= A, Start= 270, End= 277, Modeling


λ-phage head protein D (1C5E:AB, A82-93) (12-residues)
INPUT: ID= 1C5E:AB, Chain= A, Start= 82, End= 93, Modeling


TEM1 beta-lactamase (1BTL:A, A50-57) (8-residues)
INPUT: ID= 1BTL:A, Chain= A, Start= 50, End= 57, Modeling


Shaker K+ channel T1 (1T1D:A, A127-138) (12-residues)
INPUT: ID= 1T1D:A, Chain= A, Start= 127, End= 138, Modeling


Chitinase (Homology Model 1D2K:A, A349-354) (6-residues)
INPUT: ID*= 1D2K:A, Chain= A, Start= 349, End= 354, Modeling
*Homology Model taken from Seok's benchmark.



Serratia protease (1SRP:A, A311-322) (12-residues)
INPUT: ID= 1SRP:A, Chain= A, Start= 311, End= 322, Modeling




Rac1-SptP complex (1G4U:RS, R30-39) (10-residues)
INPUT: ID= 1G4U:RS, Chain= R, Start= 30, End= 39, Modeling


Rac1-RhoGDI complex (1HH4:AD, A30-39) (10-residues)
INPUT: ID= 1HH4:AD, Chain= A, Start= 30, End= 39, Modeling


Antibody H3 loop (1FGN:HL, H99-106) (8-residues)
INPUT: ID= 1FGN:HL, Chain= H, Start= 99, End= 106, Modeling

Antigen-Antibody H3 loop (2BDN:AHL, H99-106) (8-residues)
INPUT: ID= 2BDN:AHL, Chain= H, Start= 99, End= 106, Modeling

The improved version of the Random Coordinate Descent (RCD) algorithm is used to generate an ensemble of closed loops (up to 50K in the server) by rotation of the φ and ψ backbone dihedral angles according to detailed neighbor-dependent Ramachandran probability distributions:

Upon loop closure, the loops are evaluated using a fast coarse-grained energy function (ICOSA) and then the best 10% is selected. Finally, these lowest-scoring models are further refined using a detailed energy function (Rosetta) to obtain accurate all-atom predictions.

To perform such loop predictions you only need a minimal basic input: the atomic coordinates of the environment (PDB-file or fetch from PDB) and the boundary residue indices, sequence, and chain of the loop (Step 1). When you press the submit button you will check the job status in the queue tab (Step 3). Once job run is completed you can interactively explore the predicted models in the results tab (Step 4) and/or download them (Step 5). Optionally, advanced users are encouraged to customize RCD+ run by tuning the parameters in the advanced options panel (Step 2).

Please, introduce the following required data and then click on the submit button to perform the predictions:


(1) Upload your protein atomic structure in PDB format (v3.x) or fetch it by PDB-ID. It is mandatory to follow the PDB format avoiding non standard aminoacids (eg. no CYX, HIE etc.) and atom names. The presence of chain ID is also mandatory. The vast majority of RCD malfunctioning is due to format errors in the PDB. The fetching input format is ID:Chain(s) (In case you don't introduce any chain ID, the first chain ID found in PDB file will be considered). The fetching is very customizable. For example, introduce:
     2CMD:A to use the A chain from 2CMD entry,
     2BDN:HL to consider the antibody chains H and L of this antigen/antibody complex, or
     2BDN:AHL to consider the antigen as well (chain A).

IMPORTANT: This structure will define the loop environment for clash detection and provide the coordinates of anchor aminoacids.

(2) Introduce the chain ID and the Start (first) and End (last) residue indices of the loop. Note that these terminal residues are modeled from scratch and only the N- and C-terminal anchors (indices Start-1 and End+1) and their neighboring residues (indices Start-2 and End+2) are required, e.g. for a 8 residues loop:

Please, use the following indices for the corresponding examples (8 aminoacids long):
     A and 270-277 for 2CMD entry or
     H and 99-106 for the antigen/antibody case.
     (More examples of different loop lengths are provided in the Gallery tab.)

(3) Choose a prediction scenario:
     Native if the side-chain conformations of the loop neighborhood are reliable, e.g. building a chrystallographic missing loop or
     Modeling to also include the side-chains of the loop neighborhood in the refinement, e.g. predicting loops in homology modeling. As a rule of thumb, Modeling predictions take around three times longer than Native predictions.

(4) Type or paste the sequence of the modeled loop in one letter format (not including anchor aminoacids). This will be the sequence of all modeled loops. Alternatively, leave this field blank to automatically get the sequence from PDB coordinates. Introduce these sequences for the examples:
     LGKNGVEE for 2CMD case or
     GVFGFFDY for the antigen/antibody complex.

(4) We optionally encourage you to introduce some descriptive job name and an email address for quick results identification and access. It is highly recomended that you use the JAVA interface (JSmol box) in case you have a JAVA virtual machine enabled in the browser since the best 3D visualization performance is only achieved with JAVA. Note that this is not the same as having JavaScript activated. To maximize compatibility with all browsers and devices (Android, iPad or iPhone), please, use HTML5 interface instead (by default).


Please, only customize the advanced options if you are an expert user (click the "+" to deploy the advanced options panel).

If you are an advanced user, you may want to change default RCD+ parameters. Please, click the "+" to deploy the advanced options:

  • Number of closed loops generated (#Loops): By default, a different number of loops is sampled depending on the loop length, but other values within 1K-50K range can be selected. For example, while for 8 residues loops 5K loops are usually enough to obtain sub-angstrom predictions, for 12 residues higher values may be required (10-50K).
  • Number of closed loops to be refined (#ICOSA): Number of loops with lowest coarse-grained ICOSA energy that will be all-atom refined in Rosetta.
  • Ramachandran threshold (%Rama): This is the percentage of probability that defines the allowed regions of the Ramachandran maps used to constrain the conformational search [Ting et al. (2010)]. The default value depends on loop length and produces good results, but it can be tuned in the range [80-99.99%] to obtain better (or worse) results. You will see the effect that such changes produce in the shaded regions of Ramachandran maps once results have been computed.
  • Atomic model: Four different atomic models can be selected for clash detection in the conformational search stage: (N,Cα,C), (N,Cα,C,O), (N,Cα,C,Cβ), and the most detailed (N,Cα,C,O,Cβ). Only the indicated atoms will be considered in this stage. Note that all-atom loops will be generated and considered later in the refinement stage.
  • RCD method: The neighbor-dependent Ramachandran filter of the improved RCD method (Dunbrack) is the default option, but you can select the original simplified method (Simple) or an unconstrained version (Free) as well.

Any option available in the RCD standalone program can be added in the expert options box. Note that a maximum wall-time of 1 hour per job has been set to prevent abuse.

Inmediately upon job submission, your job will be queued in our server and you will be redirected to Queue status tab. In this tab all jobs submited to RCD+ Server are listed. Your jobs are shown in darker colors whereas those submitted by others appear in lighter colors. You can check server usage and whether any queued job is running ("r" status, green) or queued ("qw" status, orange). In case any of your jobs has been queued ("qw" status) it will run as soon as computational resources become available.



Once a standard-sized job is running ("r" status) it usually takes around 10-15 minutes to complete depending on its size. For example, the modeling of a large loop (12-residues) usually takes around 10 minutes. To avoid server overloading the wall-time of Native and Modeling jobs has been set to 1 and 2 hours, respectively.



As soon as your jobs finish they will move to the list of "Your finished jobs" for further access and a direct link will appear to redirect you to the Results of the last finished job.



In case you detect any problem in any of your submitted jobs they can be easily deleted by clicking the corresponding red cross. A "dr" status (black) will evidence that it is being deleted from queue. Note that anyone but you can delete your jobs.

Please, do not close the browser unless you have either kept track of the job ID or provided an email address, otherwise you will not be able to access your results when the web browser is closed.

Use mouse controls to interactively explore the generated loops in JSmol and customize their molecular representation and colors. For example, just drag for rotating, hold Shift key + double click for translating, or click in the palette to change the color of the selected loop(s). The user can choose between three different interfaces: Java, HTML5 and WebGL. The HTML5-javascript interface is activated by default. To activate the JAVA, first you must enable it in your web browser (details) and add frodock.chaconlab.org to the exception sites in the Java panel (details).

You can also check the structural qualitiy of the generated loops by deploying the More information section.

Only if you included the native loop in the PDB (just for benchmarking purposes) the result error in RMSD is evaluated and plotted versus the loop energy for all loop models.

Finally, all computed results are freely avaible for download:


  • All refined loops: All-atom refined models as a single Multi-PDB file.
  • All closed loops: All closed loop models produced by RCD+ (before any Rosetta refinement) at selected Coarse-Graining level (a single Multi-PDB file too).
  • Dunbrack plots: Neighbor-dependent Ramachandran maps, dihedral angles, and images are provided as plain text or JPG images.
  • Energy evaluation: Refinement summary table for all refined loops (plain text file) with the loop indices (#loop), the all-atom Rosetta energy before any refinement for the full protein (E_full) and the loop (E_loop), the all-atom Rosetta energy after refinement (E_full2), the RMSDs before (before E_full2 column) and after (after E_full2 column) refinement considering N,Cα,C,O atoms (R_rcd and R_BBO), N,Cα,C (R_BB), all heavy atoms (R_HA), all side-chain heavy atoms (R_SC), and all atoms including hydrogens (R_ALL).
  • Summary results: RCD+'s output summary.
  • Log-file: Plain text log file with the start/end time for each of the protocol steps.
  • All computed files: A tar+gzip file containing all job data.

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