Setting the Job Name
Give your job a name. This name will be attached to refinement results and used as an identifier. Only alphanumeric characters, dashes and underscores are allowed. Any invalid characters will be ignored.
Entering your Email
You can choose to enter an optional email address where the refinement results will be sent. Structure refinement jobs usually take few minutes to complete. We will email you a notification when the job does complete, or if it stops before completion.
Providing Initial Structure
Copy and paste or upload a protein structure for refinement into the designated areas. Please make sure to upload the structure in PDB format containing 20 standard amino acids only.
Indicating Post Refinement Model Analysis
Optioning model structure analysis is available with MolProbity and RWPlus. You can choose to include analysis of either or both tools. The default is both tools on. Including post refinement analysis takes negligible additional computation time. Results are included in job folder and are presented in table on results page.
Starting the Job
When you are ready to launch the job, use the Submit button at the bottom of the page. The job will be submitted for processing if there are no problems or missing pieces.
Monitoring Job Status
3Drefine provides web-based interactive status update and automatically redirects the user as the status changes from QUEUED to EXECUTING and finally to FINISHED. After a job is finished, the refinement results can be viewed in the web. In case the job fails, the user is intimated about the FAILED status of the job along with a possible cause of the failure.
3Drefine is computationally very efficient. The web server utilizes the iterative version of 3Drefine protocol that typically requires less than 5 minutes of computation for a protein of typical length (300 residues) for a single iteration and therefore needs around 25 minutes to generate 5 refined models. However, the turn around time of your modeling job is directly proportional to the size of the protein submitted for refinement as well as the server load. If too many jobs are accumulated in the queue, the procedure may take longer time than usual.
After a job is completed, the refinement results can be viewed in the results page containing the initial and refined structures along with job statistics like predicted quality scores of refinement models, similarity and deviation of the refined structures with respect to the supplied input structure. User may download the individual structures by clicking on them. A complete compressed achieve of the job is also made available in the web and also sent by email if specified.
Using the Results Table
On the results page a comprehensive table containing statistical results and actions for each model is displayed. Included are the 3Drefine scores, GDT-HA, GDT-TS, and RMSD scores, as well as MolProbity and RWPlus scores if selected. By default the table is sorted by ascending order by RWPlus score if selected, or by ascending order of MolProbity score, if selected, or by ascending order of 3Drefine score. The table can be reordered by any of the statistics provided by clicking on the column header. The table can then be reverse ordered by clicking the same column header again.
3Drefine provides web-based interactive visualizations of refined and initial models. Visualizations are included through the JSmol library with built in options and tools to analyze and customize models.
JSmol provides built in access to Jmol functions for analyzing and customizing models. To rotate the visualized models, click and drag the cursor over the model. To zoom in and out, place the cursor over the model and scroll in or out. For advanced Jmol functions, right click over the model. This will pop up a menu which provides additional features and options. To type Jmol commands manually enter the Jmol console by right clicking the model and selecting "console" at the bottom. For more information on what Jmol can do visit the Jmol site.
R E F E R E N C E S:
3. Bhattacharya, D., Nowotny, J., Cao, R., Cheng, J. (2016) 3Drefine: an interactive web server for efficient protein structure refinement. Nucleic Acids Research. Web Server Issue. doi: 10.1093/nar/gkw336.
2. Bhattacharya, D., Cheng, J. (2013) i3Drefine software for protein 3D structure refinement and its assessment in CASP10. PLOS ONE. 8(7): e69648.
1. Bhattacharya, D., Cheng, J. (2012) 3Drefine: Consistent Protein Structure Refinement by Optimizing Hydrogen Bonding Network and Atomic Level Energy Minimization. Proteins: Structure, Function, and Bioinformatics. 81(1): 119-131.