Permol

PERMOL is a program for semi automated homology modeling of proteins. It is based on restraint molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry weighted mean angles and their standard deviations are used. The overall long range contacts are established via a small number of distance restraints between atoms involved in hydrogen bonds and backbone atoms of conserved residues.

The complete process of homology modeling with PERMOL is interactive allowing the user to precisely control the modeling procedure at each stage. A graphical user interface affords ease of use and clearness.

PERMOL employs restraint molecular dynamics programs which are commonly used for the determination of three-dimensional structures based on experimental restraints derived from nuclear magnetic resonance (NMR) experiments. Thus homology modeling with PERMOL is especially suited to aid in the process of structure determination and to validate incomplete NMR datasets.

Authors: Andreas Möglich, Daniel Weinfurtner, Till Maurer, Wolfram Gronwald and Hans Robert Kalbitzer

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Downloading PERMOL is free of charge. However, to get access to the download area registration is required once. Within a short time you will receive an email notification with the login details.

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