# MPI-I-95-1-023

## An algorithm for the protein docking problem

### Lenhof, Hans-Peter

**MPI-I-95-1-023**. August** **1995, 11 pages. | Status:** **available - back from printing | Next --> Entry | Previous <-- Entry

Abstract in LaTeX format:

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.

Acknowledgement:** **

References to related material:

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**BibTeX**
`@TECHREPORT{``Lenhof95``,`

` 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},`

`}`