METHODS FOR COMPARISON OF PROTEIN THREE DIMENSIONAL STRUCTURE
METHODS FOR COMPARISON OF PROTEIN THREE DIMENSIONAL STRUCTURE
批准号:
5203629
负责人:
S H BRYANT
金额:
$0.0万
依托单位国家:
美国
项目类别:
财政年份:
--
资助国家:
美国
项目状态:
未结题
起止时间:
至
中文摘要
我们开发了蛋白质三维比较的算法
英文摘要
We have developed algorithms for comparison of protein three dimensional
structures. The "VAST" algorithm, for "vector alignment search tool,"
identifies substructures similarities rapidly by comparing the types,
connectivity, and relative orientations secondary structure elements.
Work has focused in three areas: 1) definition of the threshold
similarity statistic, 2) validation of sensitivity and specificity, and
3) development of statistical criteria for "optimal" residue-by-residue
alignment. VAST ranks substructure similarities by chance-occurrence
likelihood. This is calculated as the product of the probabilities that
independent element-pair superposition residuals would be observed by
chance, as determined by reference to an empirical distribution based on
random draws of element pairs in the structural database. A threshold
statistic is given as the product of the greatest substructure likelihood
and the number of possible substructure choices, as determined by a
combinatorial formula involving the number of discrete elements present
in each protein. If small, this value is interpretable directly as a
test statistic or p-value for significant similarity. VAST has been
tested by an all-against-all analysis of known structures. Sensitivity
with respect to BLAST "hits" is 99.5%. Specificity in test cases from
the literature appears perfect, and comparison to existing non-
statistical methods indicates fewer hits, with omissions being low-score
marginal similarities. Residue-residue alignments are now constructed
by a Gibb's sampling scheme, which proved more efficient than Metropolis
sampling. Significance of alternative residue alignments is evaluated
by reference to an empirical distribution of superposition residuals in
random alignments, to identify the most surprising one. An analytical
density function fitted to empirical random-element self comparison
residuals proved superior to a substructure-specific null model in
reproducing literature expert alignments, and is in addition faster. The
significance of this work will be in extending the horizon to which
evolutionary relationship may be detected, by employing structure
comparison in place of sequence comparison alone. The results have been
made available to biologists as "structural neighbors" in the "Entrez"
browser.
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METHODS FOR COMPARISON OF PROTEIN THREE DIMENSIONAL STRUCTURE
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批准号:2578631
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
STRUCTURE PREDICTION BY PROTEIN THREADING
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批准号:5203626
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
DATABASES FOR MOLECULAR MODELING
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批准号:5203627
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
THREADING PROTIEN SEQUENCE THROUGH FOLDING MOTIF
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批准号:3845098
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
ANALYSIS OF PACKING CONTACTS IN PROTEIN CRYSTALS
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批准号:3781258
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
DATABASES FOR MOLECULAR MODELING
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批准号:3781279
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
ANALYSIS OF PACKING CONTACTS IN PROTEIN CRYSTALS
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批准号:3759296
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
PROTEIN THREADING METHODS
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批准号:6162796
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
INTERNET RESOURCES FOR MOLECULAR 3D STRUCTURE
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批准号:6162797
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
EMPIRICAL ENERGY FUNCTIONS FOR MOLECULAR MODELING
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批准号:3845097
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
STRUCTURE PREDICTION BY PROTEIN THREADING
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批准号:3781278
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
STRUCTURE PREDICTION BY PROTEIN THREADING
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批准号:3759315
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
DATABASES FOR MOLECULAR MODELING
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批准号:3759316
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
DATABASES FOR MOLECULAR MODELING
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批准号:2578630
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
PROTEIN THREADING METHODS
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批准号:2578629
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
COMPUTER SOFTWARE FOR ANALYSIS OF PROTEIN THREE-DIMENSIONAL STRUCTURE
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批准号:3845099
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
ANALYSIS OF PACKING CONTACTS IN PROTEIN CRYSTALS
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批准号:3845100
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
PROTEIN 3D STRUCTURE COMPARISON
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批准号:6162798
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
METHODS FOR COMPARISON OF PROTEIN THREE DIMENSIONAL STRUCTURE
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批准号:3759325
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项目类别:
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资助金额:$0.0万
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财政年份:--
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负责人:S H BRYANT
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依托单位:
海外基金