Severity: Warning
Message: file_get_contents(https://...@gmail.com&api_key=61f08fa0b96a73de8c900d749fcb997acc09): Failed to open stream: HTTP request failed! HTTP/1.1 429 Too Many Requests
Filename: helpers/my_audit_helper.php
Line Number: 143
Backtrace:
File: /var/www/html/application/helpers/my_audit_helper.php
Line: 143
Function: file_get_contents
File: /var/www/html/application/helpers/my_audit_helper.php
Line: 209
Function: simplexml_load_file_from_url
File: /var/www/html/application/helpers/my_audit_helper.php
Line: 3098
Function: getPubMedXML
File: /var/www/html/application/controllers/Detail.php
Line: 574
Function: pubMedSearch_Global
File: /var/www/html/application/controllers/Detail.php
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Function: pubMedGetRelatedKeyword
File: /var/www/html/index.php
Line: 316
Function: require_once
Severity: Warning
Message: Attempt to read property "Count" on bool
Filename: helpers/my_audit_helper.php
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Backtrace:
File: /var/www/html/application/helpers/my_audit_helper.php
Line: 3100
Function: _error_handler
File: /var/www/html/application/controllers/Detail.php
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Function: pubMedSearch_Global
File: /var/www/html/application/controllers/Detail.php
Line: 488
Function: pubMedGetRelatedKeyword
File: /var/www/html/index.php
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Function: require_once
The ability to predict the effect of nonsynonymous SNPs (nsSNPs) on protein function is important for the success of genetic disease association studies. Here we present a statistical geometry approach to nsSNP classification based on Delaunay tessellation, whereby the impact of nsSNPs on protein function is correlated with the change in the four-body statistical potential (DeltaQ) of the protein caused by the amino acid substitution. We observed that the DeltaQ of polymorphic proteins with disease-associated nsSNPs (daSNPs) was on average significantly lower than the DeltaQ of the proteins with neutral SNPs (ntSNPs). Clustering amino acid substitutions into conservative and nonconservative groups, and using a three-letter alphabet based on side-chain polarity showed significantly lower DeltaQ in nonconservative changes to daSNPs and when hydrophobic residues were substituted by charged or by polar residues. We also found that the daSNPs in the protein core caused much lower DeltaQ than surface daSNPs. This approach demonstrates a strong correlation between the computed DeltaQ and SNP classification. Integration of our approach with the existing models will help achieve a more precise recognition of nsSNPs that underlie polygenic diseases. All of the programs were written in Java and are available from the authors upon request.
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Source |
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http://dx.doi.org/10.1002/humu.20238 | DOI Listing |
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