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Original scientific paper

Molecular Surface Walk

Janez Konc
Milan Hodošček
Dušanka Janezić


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Abstract

A new algorithm to compute a solvent accessible molecular surface (MS) and a graphical computer program for a molecular surface walk have been designed. The surface is generated by rolling a spherical probe representing a solvent molecule over the atoms of the investigated molecule. This surface representation is used in the graphical computer program MS walk to achieve a new way of viewing the molecules. The advantage of the MS walk approach is that the molecular cavities, only partially visible by other methods, can be inspected. The new algorithm’s performance is comparable to that of similar existing algorithms and its time complexity is linear with respect to the number of atoms. The MS algorithm and the MS walk program can be accessed on the Web (http://www.cmm.ki.si/konc/ms_walk).

Keywords

solvent accessible surface; molecular graphics; algorithm

Hrčak ID:

4154

URI

https://hrcak.srce.hr/4154

Publication date:

19.7.2006.

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