Abstract：
:We have developed a new method for the prediction of peptide sequences that bind to a protein, given a three-dimensional structure of the protein in complex with a peptide. By applying a recently developed sequence prediction algorithm and a novel ensemble averaging calculation, we generate a diverse collection of peptide sequences that are predicted to have significant affinity for the protein. Using output from the simulations, we create position-specific scoring matrices, or virtual interaction profiles (VIPs). Comparison of VIPs for a collection of binding motifs to sequences determined experimentally indicates that the prediction algorithm is accurate and applicable to a diverse range of structures. With these VIPs, one can scan protein sequence databases rapidly to seek binding partners of potential biological significance. Overall, this method can significantly enhance the information contained within a protein- peptide crystal structure, and enrich the data obtained by experimental selection methods such as phage display.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Wollacott AM,Desjarlais JRdoi
10.1006/jmbi.2001.5035keywords:
subject
Has Abstractpub_date
2001-10-19 00:00:00pages
317-42issue
2eissn
0022-2836issn
1089-8638pii
S0022-2836(01)95035-1journal_volume
313pub_type
杂志文章abstract：:Spider dragline silk, one of the strongest polymers in nature, is composed of proteins termed major ampullate spidroin (MaSp) 1 and MaSp2. The N-terminal (NT) domain of MaSp1 produced by the nursery web spider Euprosthenops australis acts as a pH-sensitive relay, mediating spidroin assembly at around pH 6.3. Using ami...
journal_title：Journal of molecular biology
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journal_title：Journal of molecular biology
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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pub_type： 杂志文章
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