TY - JOUR
T1 - Extraction of well-fitting substructures
T2 - Root-mean-square deviation and the difference distance matrix
AU - Lesk, Arthur M.
PY - 1997
Y1 - 1997
N2 - The extraction of well-fitting substructures of two or more sets of proteins has applications to analysis of mechanisms of conformational change in proteins, including pathways of evolution, to classification of protein folding patterns, and to evaluation of protein structure predictions. Many methods are known for extracting some substantial common substructure with low root-mean-square deviation (r.m.s.d.). A harder problem is addressed here: finding all common substructures with r.m.s.d. less than a prespecified threshold. Our approach is to consider the minimum value of the maximum distance between corresponding points, corresponding to superposition in the Chebyshev norm. Using the properties of Chebyshev superposition, we derive relationships between the r.m.s.d. and the maximum element of the difference matrix, two common measures of structural similarity. The results provide a basis for developing algorithms and software to identify all well-fitting subsets.
AB - The extraction of well-fitting substructures of two or more sets of proteins has applications to analysis of mechanisms of conformational change in proteins, including pathways of evolution, to classification of protein folding patterns, and to evaluation of protein structure predictions. Many methods are known for extracting some substantial common substructure with low root-mean-square deviation (r.m.s.d.). A harder problem is addressed here: finding all common substructures with r.m.s.d. less than a prespecified threshold. Our approach is to consider the minimum value of the maximum distance between corresponding points, corresponding to superposition in the Chebyshev norm. Using the properties of Chebyshev superposition, we derive relationships between the r.m.s.d. and the maximum element of the difference matrix, two common measures of structural similarity. The results provide a basis for developing algorithms and software to identify all well-fitting subsets.
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U2 - 10.1016/S1359-0278(97)00057-6
DO - 10.1016/S1359-0278(97)00057-6
M3 - Article
C2 - 9218960
AN - SCOPUS:0030628746
VL - 2
SP - S12-S14
JO - Folding and Design
JF - Folding and Design
SN - 1359-0278
IS - 3
ER -