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Energy minimisation of side chains

Here we offer the possibility to refine the side-chains conformations; it works in dihedral angle space, using the chi angles as variables.
The backbone atoms will remain fixed in this context. Only a van der Waals-like energy is taken into account at this stage.

Briefly stated, the advantage of working in dihedral angle space is that there are about 8 times less variables than in cartesian space; hence a considerable gain in cpu time.

Here we use standard Conjugate Gradient minimisation with Noguti and Go algorithm for analytical evaluation of the derivatives of the energy function w.r.t. dihedral angles (see Abe, Brown, Noguti and Go, Comp. & Chem., 1984, 8:239-247).

Also, instead of classical Lennard-Jones vdW potentials, here Michael Levitt's soft potentials are used (see J.Mol. Biol., 1983, 170, 723-64).

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Job title (Only alphanumerical characters)

PDB input file Ex: Example

Input data formats

  • The job title is just for your own identification, but note that it will show up in the public job queue (but your results will not be public).

  • The coordinate file should be in PDB format, with only a single structure (no multiple models). Atoms marked with alternate residue flags will be removed.
    Proline residues are not entirely correctly handled in this version of the algorithm. You may want to regularize their conformations afterwards...

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 15:48 March 02, 2009.