In-Geol Choi, Jaimyoung Kwon, and Sung-Hou Kim, UC Berkeley

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Presentation transcript:

In-Geol Choi, Jaimyoung Kwon, and Sung-Hou Kim, UC Berkeley Local feature frequency profile: A method to measure structural similarity in proteins In-Geol Choi, Jaimyoung Kwon, and Sung-Hou Kim, UC Berkeley PNAS 2004 presented by Chao Wang

Abstract

Background Protein classification Protein alignment SCOP CATH DALI CE VAST SSAP

Background cont'd Protein structure universe

Methods

Database

Local Feature (LF)

LF cont'd

SVD for visualization

Results How to select the parameters? m=10, K=100

100 clusters

Why use normalization?

Visualization

Visualization cont'd

Comparison with SCOP/CATH

Special case

Discussion

Comments by Chao To design features in our NN ...