Comprehensiveevaluationofproteinstructurealignment.pptVIP

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures Rachel Kolodny Patrice Koehl Michael Levitt Stanford University The Structural Alignment Problemcomparison of structures Two chains in R3 A=(a1,a2,…,an), B=(b1,b2,…,bm) Find sub-chains sa and sb s.t. - (asa(1),asa(2),…, asa(k)),(bsb(1),bsb(2),…, bsb(k)) are similar k is maximal Similarity in Structure Two common similarity measures cRMS dRMS Alignment Scoressingle number that allows comparison of two alignments Given two alignments, judging which is better We have: length k , cRMS U