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ADAPT: A molecular mechanics approach for studying the structural properties of long DNA sequences
Author(s) -
Lafontaine Ingrid,
Lavery Richard
Publication year - 2000
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/1097-0282(2000)56:4<292::aid-bip10028>3.0.co;2-9
Subject(s) - dna , base pair , sequence (biology) , energy minimization , dna sequencing , computational biology , molecular mechanics , chemistry , a dna , genome , nucleotide , algorithm , biological system , molecular dynamics , gene , computational chemistry , computer science , biology , biochemistry
We describe an original approach to determining sequence–structure relationships for DNA. This approach, termed ADAPT, combines all‐atom molecular mechanics with a multicopy algorithm to build nucleotides that contain all four standard bases in variable proportions. These nucleotides enable us to search very rapidly for base sequences that energetically favor chosen types of DNA deformation or chosen DNA–protein or DNA–ligand interactions. Sequences satisfying the chosen criteria can be found by energy minimization, combinatorial sequence searching, or genome scanning, in a manner similar to the threading approaches developed for protein structure prediction. In the latter case, we are able to analyze roughly 2000 base pairs per second. Applications of the method to DNA allomorphic transitions, DNA deformation, and specific DNA interactions are presented. © 2001 John Wiley & Sons, Inc. Biopolymers (Nucleic Acid Sci) 56: 292–310, 2001