期刊
JOURNAL OF PHYSICAL CHEMISTRY B
卷 116, 期 29, 页码 8494-8503出版社
AMER CHEMICAL SOC
DOI: 10.1021/jp212541y
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资金
- National Institute of General Medical Sciences [R01 GM44557]
- Center for Theoretical Biological Physics
- NSF [PHY-0822283, CHE-0846701]
- Camille Dreyfus Teacher-Scholar Award
- Arnold and Mabel Beckman Foundation
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [0835824] Funding Source: National Science Foundation
- Direct For Mathematical & Physical Scien
- Division Of Physics [1308264] Funding Source: National Science Foundation
The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained protein force field. AWSEM contains physically motivated terms, such as hydrogen bonding, as Well as a bioinformatically based local structure biasing term, which efficiently takes into account many-body effects that are modulated by the local sequence. When combined with appropriate local or global alignments to choose memories, AWSEM can be used to perform de novo protein structure prediction. Herein we present structure prediction results for a particular choice of local sequence alignment method based on short residue sequences called fragments. We demonstrate the model's structure prediction capabilities for three levels of global homology between the target sequence and those proteins used for local structure biasing, all of which assume that the structure of the target sequence is not known. When there are no homologues in the database of structures used for local structure biasing, AWSEM calculations produce structural predictions that are somewhat improved compared with prior works using related approaches. The inclusion of a small. number of structures from homologous sequences improves structure prediction only marginally, but when the fragment search is restricted to only homologous sequences, AWSEM can perform high resolution structure prediction and can. be used for kinetics and dynamics studies.
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