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Original scientific paper

Molecular Surface Walk

Janez Konc
Milan Hodošček
Dušanka Janezić

Full text: english pdf 209 Kb


page 237-241

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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 (


solvent accessible surface; molecular graphics; algorithm

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