Help

  • E-mail address

    If an e-mail address is entered here, it will be used to notify you when the job has completed. (Unlike older versions of ModLoop, the PDB file is not emailed directly to you, but can be downloaded from this web site.)

  • MODELLER key

    This server is freely available for academic users. The loop modeling module is implemented in the MODELLER program, therefore you need to register for a license of MODELLER. It can be done online and automatically by accessing the MODELLER web site. The web site will email you a MODELLER key. You need to enter this license key here in order to use this server.

  • Upload your file

    The uploaded coordinate file must be a valid PDB format file. The loop region to be modeled must be included in the coordinate file, since the amino acid sequence and initial loop energy are derived from the PDB file. (You can give the loop atoms dummy coordinates, but each atom must have different coordinates, or you will get a 'Central bond too short' error from Modeller.)

  • Select loop segment

    The starting and ending residue positions and chain identifiers (if any) should be specified here, separated by ":". One can specify several loop segments, but the total number of residues involved in the loops must not exceed 14. Only regular amino acids can be selected for loop modeling (i.e. no non-standard residues such as ligands, DNA strands, etc.) although the non-loop regions of your PDB can contain non-standard residues. Please use the following syntax:

    Example 1. one loop between residues 12 and 18 in chain B:

    12:B:18:B:

    Example 2. one loop between residues 15 and 22, no chain identifier, another loop between residues 98 and 103 in chain B and one more residue, at position 66 in chain C to be selected:

    15::22::
    98:B:103:B:
    66:C:66:C:
    

    Note that ModLoop refines the position of residues that already exist in your PDB file - it does not add missing residues (if you want to do that, add the residues with dummy coordinates yourself first).

  • Name of the model

    The name entered here is used to identify your job in the ModLoop system.


Common errors

  • 'Central bond too short': this is usually caused by having two or more atoms in your input PDB file with the same coordinates. (Tip: if you don't know the original coordinates of your loop, specify dummy coordinates, but don't put every atom at (0,0,0).)
  • 'some selected residues have no topology': the loop modeling protocol is only defined on standard amino acids. Thus, you can't select residues for modeling which have no defined MODELLER topology, such as DNA/RNA, metal ions, or ligands.
  • 'loop too long': this can happen if your PDB file residues are not sequential, or the chains are interleaved. MODELLER reads PDB files strictly sequentially, so if your PDB file contains residues 1-100 in chain A, followed by 1-100 in chain B, followed by 101-200 in chain A, and your loop selection is 99:A:101:A:, MODELLER will actually try to model the entire B chain (since it falls between residues 99 and 101 in chain A). This is probably not what you intended. In this case, the easiest solution is to reorder the PDB file in a text editor to stick the two parts of chain A together.

Running ModLoop locally

The ModLoop protocol is part of Modeller, which can be downloaded from our website and is free for academic use. An example Modeller script for loop refinement can be found in the Modeller manual. ModLoop simply builds 300 models with Modeller, and then returns the single model with the lowest molpdf score.