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- W2142727530 abstract "Conventionally, protein structure prediction via “threading” relies on some nonoptimal method to align a protein sequence to each member of a library of known structures. We show how a score function (force field) can be modified so as to allow the direct application of a dynamic programming algorithm to the problem. This involves an approximation whose damage can be minimized by an optimization process during score function parameter determination. The method is compared to sequence to structure alignments using a more conventional pair-wise score function and the frozen approximation. The new method produces results comparable to the frozen approximation, but is faster and has fewer adjustable parameters. It is also free of memory of the template's original amino acid sequence, and does not suffer from a problem of nonconvergence, which can be shown to occur with the frozen approximation. Alignments generated by the simplified score function can then be ranked using a second score function with the approximations removed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1455–1467, 1999" @default.
- W2142727530 created "2016-06-24" @default.
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- W2142727530 date "1999-11-15" @default.
- W2142727530 modified "2023-10-13" @default.
- W2142727530 title "Protein sequence threading, the alignment problem, and a two-step strategy" @default.
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- W2142727530 doi "https://doi.org/10.1002/(sici)1096-987x(19991115)20:14<1455::aid-jcc1>3.0.co;2-d" @default.
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