TY - GEN
T1 - Using microenvironments to identify allosteric binding sites
AU - Foley, Christopher Eric
AU - Al Azwari, Sana Mohammad M
AU - Dufton, Mark
AU - Wilson, John
PY - 2012/10/4
Y1 - 2012/10/4
N2 - Protein amino acid residues can be classified by their chemical properties and data mining can be used to make predictions about their structure and function. However, the properties of the surrounding residues contribute to the overall chemical context. This paper defines microenvironments as the spherical volume around a point in space and uses these volumes to determine average properties of the encompassed residues. The approach to index generation rapidly constructs microenvironment data. The averaged chemical properties are then employed in allosteric site prediction using support vector machines and neural networks. The results show that index generation performs best when microenvironment radius matches the granularity of the index and that microenvironments improve the classification accuracy.
AB - Protein amino acid residues can be classified by their chemical properties and data mining can be used to make predictions about their structure and function. However, the properties of the surrounding residues contribute to the overall chemical context. This paper defines microenvironments as the spherical volume around a point in space and uses these volumes to determine average properties of the encompassed residues. The approach to index generation rapidly constructs microenvironment data. The averaged chemical properties are then employed in allosteric site prediction using support vector machines and neural networks. The results show that index generation performs best when microenvironment radius matches the granularity of the index and that microenvironments improve the classification accuracy.
KW - neural networks
KW - microenvironments
KW - allosteric binding sites
KW - bioinformatics
UR - http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6373898
UR - http://www.scopus.com/record/display.url?eid=2-s2.0-84872526650&origin=inward&txGid=F58F98FE25389759CA2C5FD5BBBB4640.53bsOu7mi7A1NSY7fPJf1g%3a1
U2 - 10.1109/BIBM.2012.6392711
DO - 10.1109/BIBM.2012.6392711
M3 - Conference contribution book
SN - 9781467325592
SP - 411
EP - 415
BT - 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012)
PB - IEEE
CY - Piscataway, NJ
T2 - 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012)
Y2 - 4 October 2012 through 7 October 2012
ER -