AMBER Archive (2001)

Subject: Re: your mail

From: Krzysztof Murzyn (ubmurzyn_at_cyf-kr.edu.pl)
Date: Thu Feb 22 2001 - 04:45:36 CST

> has anybody an idea how to measure a volume of the cavity inside protein
> along MD trajectry?
>
Hi,

There's an excelent (and accurate) way to perform such calculations. The
analytic way to compute surface and volume of cavities in molecular
systems was published in Liang et al. Proteins, 1998, 33:1-17 (there're in
fact two articles, the first describes the method - alpha shapes, the
second shows an application..).

Regards,

Krzysztof