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An algorithm for the protein docking problem

Lenhof, Hans-Peter

August 1995, 11 pages.

Status: available - back from printing

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

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  AUTHOR = {Lenhof, Hans-Peter},
  TITLE = {An algorithm for the protein docking problem},
  TYPE = {Research Report},
  INSTITUTION = {Max-Planck-Institut f{\"u}r Informatik},
  ADDRESS = {Im Stadtwald, D-66123 Saarbr{\"u}cken, Germany},
  NUMBER = {MPI-I-95-1-023},
  MONTH = {August},
  YEAR = {1995},
  ISSN = {0946-011X},