**************** The 2nd., Lab Seminar ****************************

Date: Thu, May 8, 2008  PM 2:30-

Place: No.616 Seminar room
　　　　　　 Graduate School of Information Science

Speaker: Isseki Yu

Title: Extracting Hydration Sites around Proteins from Explicit 
Water Simulations
RICHARD H. HENCHMAN, J. ANDREW MCCAMMON
J. Comput. Chem., 23, 861 (2002).

Abstract:
 Two new methods are assessed for determining the location of hydration 
sites around proteins from computer simulation. Current methods extract 
hydration sites from peaks in the water density constructed in the 
protein frame. However, the dynamic nature of the water molecules, 
the nearby protein residues, and the protein reference frame as a 
whole tend to smear out the water density, making it more difficult 
to resolve sites. Two techniques are introduced to better resolve the 
water density. The first is to construct the water density from the 
time-averaged position of each water molecule in the protein frame 
while the water remains within a given distance of this averaged 
position. The second technique is to construct the water density 
from the time-averaged position of each water in the reference frame 
only of the nearby residues. Criteria for determining hydration sites 
from the water density are examined. Both techniques are found to 
significantly improve the detail in the water density and the number 
of hydration sites detected. 

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