Weighting features to recognize 3D patterns of electron density in X-ray protein crystallography.
Feature selection and weighting are central problems in pattern recognition and instance-based learning. In this work, we discuss the challenges of constructing and weighting features to recognize 3D patterns of electron density to determine protein structures. We present SLIDER, a feature-weighting algorithm that adjusts weights iteratively such that patterns that match query instances are better ranked than mismatching ones. Moreover, SLIDER makes judicious choices of weight values to be considered in each iteration, by examining specific weights at which matching and mismatching patterns switch as nearest neighbors to query instances. This approach reduces the space of weight vectors to be searched. We make the following two main observations: (1) SLIDER efficiently generates weights that contribute significantly in the retrieval of matching electron density patterns; (2) the optimum weight vector is sensitive to the distance metric i.e. feature relevance can be, to a certain extent, sensitive to the underlying metric used to compare patterns.
Gopal
Kreshna
K
Department of Computer Science, Texas A&M University, USA. kgopal@cs.tamu.edu
Romo
Tod D
TD
Sacchettini
James C
JC
Ioerger
Thomas R
TR
D015502:Absorptiometry, Photon / Q000379:methods*; D000465:Algorithms; D001185:Artificial Intelligence; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods*; D004583:Electrons; D021621:Imaging, Three-Dimensional / Q000379:methods; D008956:Models, Chemical; D008958:Models, Molecular; D010363:Pattern Recognition, Automated / Q000379:methods; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure*; D012984:Software
D011506:Proteins