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Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure

Abstract:

The difficulties encountered in sampling of systems with rough energy landscapes using present methodology significantly limit the impact of simulation on molecular biology, in particular protein folding and design. Here, we present a major methodological development based on a promising new technique, the reference potential spatial warping algorithm (REPSWA) [Z. Zhu et al., Phys. Rev. Lett., 88 (2002), pp. 100201-100204], and present applications to several realistic systems. REPSWA works b...

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Publisher copy:
10.1137/070686706

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Journal:
SIAM Journal on Scientific Computing
Volume:
30
Issue:
4
Pages:
2055-2083
Publication date:
2007-01-01
DOI:
EISSN:
1095-7197
ISSN:
1064-8275
URN:
uuid:b678c2dd-5593-4a3b-96f0-3ef382f3e021
Source identifiers:
380099
Local pid:
pubs:380099
Language:
English
Keywords:

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