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Optimised amino acid specific weighting factors for unbound protein docking.

ABSTRACT: BACKGROUND: One of the most challenging aspects of protein-protein docking is the inclusion of flexibility into the docking procedure. We developed a postfilter where the grid-representation of proteins for docking is extended by an optimised weighting factor for each amino acid. RESULTS: For up to 86% of the evaluated complexes a near-native structure was within the top 5% of the ranked prediction output. The weighting factors obtained by the optimisation procedure correlate to a certain extent with the flexibility of the amino acids, their hydrophobicity and with their propensity to be in the interface. CONCLUSION: Use of the optimised amino acid specific parameters yields a strong increase of near-native structures on the first ranks of the prediction.

SUBMITTER: Heuser P

PROVIDER: S-EPMC1534072 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature

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Optimised amino acid specific weighting factors for unbound protein docking.

Heuser Philipp P Schomburg Dietmar D

BMC bioinformatics 20060714

<h4>Background</h4>One of the most challenging aspects of protein-protein docking is the inclusion of flexibility into the docking procedure. We developed a postfilter where the grid-representation of proteins for docking is extended by an optimised weighting factor for each amino acid.<h4>Results</h4>For up to 86% of the evaluated complexes a near-native structure was within the top 5% of the ranked prediction output. The weighting factors obtained by the optimisation procedure correlate to a c ...[more]

PMID: 16842615

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Project description:Compound-specific isotope analysis (CSIA) of amino acids (AAs) in consumer tissues is a developing technique with wide-ranging applications for identifying nitrogen (N) sources and estimating animal trophic level. Controlled experiments are essential for determining which dietary conditions influence variability in N stable isotopes (?15N) trophic enrichment factors in bulk tissue (TEFbulk) and AAs (TEFAA). To date, however, studies have not independently evaluated the effect of protein quantity and quality (digestibility) on TEFs, complicating the application of AA-?15N values for estimating trophic levels. We conducted a 98-d feeding experiment using five formulated isoenergetic feeds prepared with a high-quality protein source to evaluate the effect of protein quantity and quality on TEFs of liver and muscle tissues of juvenile Pacific yellowtail (Seriola lalandi), a carnivorous fish species. We decreased protein digestibility using well-established protocols that do not change AA profiles. Growth rates were higher in diets with higher protein content, and isotopic equilibrium was reached for both fish tissues and all treatments. Protein quantity and quality influenced isotope discrimination depending on tissue type and AA. In liver tissue, bulk TEFs showed a limited but significant relationship with protein quality, but did not differ with protein quantity or quality in muscle. None of the pre-established source AAs (Lys, Met, Phe, and Gly) TEFs varied significantly with protein quantity or quality in liver tissue. However, in muscle tissue, TEFPhe increased significantly with protein content and decreased in response to reduced digestibility, indicating it may not serve as proxy for baseline isotopic values used to calculate trophic level. Among trophic AAs, TEFLeu decreased significantly with increasing protein quantity in liver tissue, while both Leu and Ile TEFs decreased with lower protein digestibility in muscle tissue. Our results indicate that CSIA-AA in liver tissue provides more robust source and trophic AA-?15N values than in muscle.

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Optimised amino acid specific weighting factors for unbound protein docking.

Publications

Optimised amino acid specific weighting factors for unbound protein docking.

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