de.mpg.escidoc.pubman.appbase.FacesBean
Deutsch
 
Hilfe Wegweiser Impressum Kontakt Einloggen
  DetailsucheBrowse

Datensatz

DATENSATZ AKTIONENEXPORT

Freigegeben

Bericht

An algorithm for the protein docking problem

MPG-Autoren
http://pubman.mpdl.mpg.de/cone/persons/resource/persons44909

Lenhof,  Hans-Peter
Algorithms and Complexity, MPI for Informatics, Max Planck Society;

Externe Ressourcen
Es sind keine Externen Ressourcen verfügbar
Volltexte (frei zugänglich)

MPI-I-95-1-023.pdf
(beliebiger Volltext), 9MB

Ergänzendes Material (frei zugänglich)
Es sind keine frei zugänglichen Ergänzenden Materialien verfügbar
Zitation

Lenhof, H.-P.(1995). An algorithm for the protein docking problem (MPI-I-1995-1-023). Saarbrücken: Max-Planck-Institut für Informatik.


Zitierlink: http://hdl.handle.net/11858/00-001M-0000-0014-A1E1-3
Zusammenfassung
We have implemented a parallel distributed geometric docking algorithm that uses a new measure for the size of the contact area of two molecules. The measure is a potential function that counts the ``van der Waals contacts'' between the atoms of the two molecules (the algorithm does not compute the Lennard-Jones potential). An integer constant $c_a$ is added to the potential for each pair of atoms whose distance is in a certain interval. For each pair whose distance is smaller than the lower bound of the interval an integer constant $c_s$ is subtracted from the potential ($c_a <c_s$). The number of allowed overlapping atom pairs is handled by a third parameter $N$. Conformations where more than $N$ atom pairs overlap are ignored. In our ``real world'' experiments we have used a small parameter $N$ that allows small local penetration. Among the best five dockings found by the algorithm there was almost always a good (rms) approximation of the real conformation. In 42 of 52 test examples the best conformation with respect to the potential function was an approximation of the real conformation. The running time of our sequential algorithm is in the order of the running time of the algorithm of Norel {\it et al.}[NLW+]. The parallel version of the algorithm has a reasonable speedup and modest communication requirements.