Knowledge-based Potential Refinement for Proteins
What is the KoBaMIN server?
The KoBaMIN server is an internet service for very fast protein structure refinement. The refinement protocol is composed of two steps: (1) energy minimization using a knowledge-based potential of mean force and (2) stereochemistry correction. Users submit one or more protein structures and KoBaMIN likely brings them closer to the native-like conformation.
How does it work?
Step 1. The user provides initial protein structure(s) for refinement and a reference structure (optional).
The reference structure is used in calculation of CαRMSD, GDT-HA and GDT-TS.
If no reference structure is provided, the initial structure is used for these calculations.
All structures are checked for the correct file types. If successful, the job is queued, and the user receives a notification message if he provided an email address. Otherwise, the user is shown an error message detailing the error.
Step 2. Structural integrity checks are done using BioPython (Bio.PDB module) and incorrectly formatted PDB files are filtered out. We follow the Protein Data Bank convention for the PDB format. Insertion codes are dealt with in the following way: only the first instance of every residue is kept (e.g. 55, 55A; 61A, 61B). Insertion codes are then removed from the PDB file.
Step 3. Structures undergo refinement through energy minimization using a statistical knowledge-based potential of mean force (KB01). This is the major refinement process of the protocol.
Step 4. (optional) MESHI is used to give stereo-chemically correct models. This can be turned off by unchecking the box at the input page. It focuses on four criteria:
Figure 1. Schematic Representation of the KoBaMIN protocol.
Step 5.For each structure, CαRMS, GDT-HA, and GDT-TS are calculated either from the provided reference structure or, in its absence, from its initial structure. These are merely informational. Although it is highly likely that a structure moves towards the native state, sometimes the protocol fails to do so. Please refer to the Proteins paper below for more details.
Step 6. All data is organized, archived, and made available for download. An email is sent to the user notifying of job completion. The results are deleted from our server seven days after job completion.
What is the output of the KoBaMIN server?
Upon completion of the job, the server generates a results page displaying all the submitted structures and their respective analysis values. An example results page is available here.
If an email was provided on submission, the user is sent links to the abovementioned results page and to two ZIP archives (an example is shown in the links below):
The full data archive (jobname.zip) is structured in several folders:
How to cite the KoBaMIN server?
Further questions or suggestions?
Please email us at gauravchopra [.at.] alumni [.dot.] stanford [.dot.] edu