A Tool for Optimal Structure Alignment of Molecules
Date Issued
2004
Date
2004
Author(s)
Chang, Pei-Ken
DOI
en-US
Abstract
Recently, developments have been made in finding the common substructures in proteins because the shape of a protein is highly related to its functions. With the help of the analyzing tools, a user can find out functional and evolutional relationships among proteins. However, it has been recently discovered that there are shared structural features between protein structures and RNA structures. The
existing tools are designed only for alignment of proteins, thus new tools need to be developed to address the above problem, that is, molecular mimicry.
We propose a tool to optimally align two molecules based on their 3D structural data, and the user can observe the result of alignment visually via the tool. In addition to finding important substructures in proteins, the tool can also align a protein and a nucleic acid, although they are two very different types of molecules.
In order to align two molecules A and B, we might extract the surface atoms of molecules before aligning by alpha-shape algorithm. Then Geometric Hashing is applied to globally find initial matching of approximately overlapped atoms, thus parts of molecule A can be matched to parts of molecule B. Next, a fine tuning process is introduced, hich is based on local optimization of overlapped parts, and the Iterative Closest Point (ICP) is used until the number of overlapped atoms within a given distance threshold can not be increased any more.
The results show that our method is useful to structurally align two molecules, not restricted to align two proteins only. Besides, our tool outperforms in terms of RMSD and number of matched atom pairs in comparison to other tools.
Subjects
蛋白質結構比對
活化區域
Protein Structure Alignment
Active Site
Type
thesis
File(s)![Thumbnail Image]()
Loading...
Name
ntu-93-R91922080-1.pdf
Size
23.31 KB
Format
Adobe PDF
Checksum
(MD5):af4ed0a5e6ea33e25c3b6074d06bf57d