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A Point-Matching Based Algorithm for 3D Surface Alignment of Drug-Sized Molecules
 

Summary: A Point-Matching Based Algorithm for 3D
Surface Alignment of Drug-Sized Molecules
Daniel Baum and Hans-Christian Hege
Zuse Institute Berlin (ZIB), Germany
{baum,hege}@zib.de
Abstract. Molecular shapes play an important role in molecular inter-
actions, e.g., between a protein and a ligand. The `outer' shape of a
molecule can be approximated by its solvent excluded surface (SES). In
this article we present a new approach to molecular surface alignment
which is capable of identifying partial similarities. The approach utilizes
an iterative point matching scheme which is applied to the points repre-
senting the SES. Our algorithm belongs to the multi-start methods. We
first generate a number of initial alignments that are locally optimized
by an iterative surface point matching algorithm which tries to maximize
the number of matched points while minimizing the distance between the
matched points. The algorithm identifies similar surface regions given by
the matched surface points. This makes it well suited for multiple align-
ment of molecular surfaces. The subalgorithm proposed for distributing
points uniformly across a surface might be of general interest for the
comparison of molecular surfaces.

  

Source: Andrzejak, Artur - Konrad-Zuse-Zentrum für Informationstechnik Berlin

 

Collections: Computer Technologies and Information Sciences