the protein threading problem with sequence amino acid interaction preferences is np-complete（线程的蛋白质序列氨基酸交互偏好是np完全问题）.pdfVIP

In press Protein Engineering The Protein Threading Problem With Sequence Amino Acid Interaction Preferences Is NPComplete Richard H Lathrop Articial Intelligence Lab oratory Massachusetts Institute of Technology Cambridge Massachusetts USA voice fax ricklaimitedu email Running title The Protein Threading Problem Is NPComplete Keywords contact p otentials inverse protein folding protein threading NPcomplete protein structure prediction sequencestructure alignment In press Protein Engineering Abstract In recent protein structure prediction research there has b een a great deal of interest in using amino acid interaction preferences eg contact p otentials or p otentials of mean force to align thread a protein sequence to a known structural motif An imp ortant op en question is whether a p olynomial time algorithm for nding the globally optimal threading is p ossible We identify the two critical conditions governing this question variablelength gaps are admitted into the alignment and interactions b etween amino acids fr om the sequence are admitted into the score function We prove that if b oth these conditions are allowed then the Protein Threading Decision Problem do es there exist a threading with a score less than K is NPcomplete in the strong sense ie is not merely a numb er problem and the related problem of nding the globally optimal protein threading is NPhard Therefore no p olynomial