This service builds a Go model from a PDB file.

Files will be provided to set up simulations in CHARMM of a simple C-alpha based model of the input protein. The topology (.top), parameter (.param), and sequence (.seq) files are to be streamed into CHARMM (in that order). A PDB file representing the native-state conformation is also provided (.pdb), as well as the list of native contacts used in building the potentials (.Qdetails).

In any publications arising from the use of this server, please reference:

    Karanicolas and Brooks, The origins of asymmetry in the folding transition states of protein L
        and protein G, Prot. Sci., v. 11, p. 2351-2361 (2002).
    Karanicolas and Brooks, Improved Go-like models demonstrate the robustness of protein
        folding mechanisms towards non-native interactions, J. Mol. Biol., v. 334, p. 309-325

For examples of applications of this server, see the above two references, as well as:

    Karanicolas and Brooks, The structural basis for biphasic kinetics in the folding of the WW
        domain from a formin-binding protein: Lessons for protein design?, Proc. Natl. Acad. Sci.
        USA, v. 100, p. 3954-3959 (2003).
    Karanicolas and Brooks, The importance of explicit chain representation in protein folding
        models: An examination of Ising-like models, Proteins, v. 53, p. 740-747 (2003).

Please provide in the form below the name of a PDB file to be uploaded from your machine, a reference TAG (for your use), and a valid email address.

The resulting gzipped tar file will be mailed to you within a few seconds. The tag will be included in the subject line.

PDB input file

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