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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Guisong Wang Kinser, J. |
| Copyright Year | 2006 |
| Description | Author affiliation: Dept. of Bioinf. & Comput. Biol., George Mason Univ., Fairfax, VA (Guisong Wang; Kinser, J.) |
| Abstract | A new perspective to investigate protein structures was introduced by applying Isomap algorithm on the protein 3-D structures. Through representing the location of each amino acid in the protein by its Calpha atom, the protein 3D structure was described as a set of points in 3D space. The reasonable nearest neighbors were defined through statistical amino acids contacts information and protein structure analysis interests. The Isomap algorithm on the 3D protein structure generated the meaningful protein geodesic structure. The residual variance analysis demonstrated that the best dimensionality for representing protein geodesic structure is 3D, but the computational results also showed that there is a nearly linear relationship between the geodesic shortest distance in original 3D and the Euclidean distance in the 2D constructed by the first two of Isomap's coordinates. The 2D protein geodesic representations can be used to measure the protein similarity and the analysis of the 2D protein geodesic representation image reveals the different protein secondary structures having different patterns. The Isomap's global coordinates provided a new approach to analyze the protein structures. |
| Starting Page | 994 |
| Ending Page | 998 |
| File Size | 5289386 |
| Page Count | 5 |
| File Format | |
| ISBN | 1424407842 |
| ISSN | 10586393 |
| DOI | 10.1109/ACSSC.2006.354901 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2006-10-29 |
| Publisher Place | USA |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | Proteins Image analysis Amino acids Nearest neighbor searches Information analysis Analysis of variance Geophysics computing Euclidean distance Level measurement Pattern analysis |
| Content Type | Text |
| Resource Type | Article |
| Subject | Signal Processing Computer Networks and Communications |
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