Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial
نویسندگان
چکیده
منابع مشابه
Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial.
Amino acid substitution models are essential to most methods to infer phylogenies from protein data. These models represent the ways in which proteins evolve and substitutions accumulate along the course of time. It is widely accepted that the substitution processes vary depending on the structural configuration of the protein residues. However, this information is very rarely used in phylogene...
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SUMMARY Protein secondary structure and solvent accessibility predictions are a fundamental intermediate step towards protein structure and function prediction. We present new systems for the ab initio prediction of protein secondary structure and solvent accessibility, Porter 4.0 and PaleAle 4.0. Porter 4.0 predicts secondary structure correctly for 82.2% of residues. PaleAle 4.0's accuracy is...
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Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a partic...
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We have improved the multiple linear regression (MLR) algorithm for protein secondary structure prediction by combining it with the evolutionary information provided by multiple sequence alignment of PSI-BLAST. On the CB513 dataset, the three states average overall per-residue accuracy, Q(3), reached 76.4%, while segment overlap accuracy, SOV99, reached 73.2%, using a rigorous jackknife procedu...
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Protein domains are considered the basic unit of protein tertiary structure. We have developed a 1D-Recursive Neural Network (1D-RNN) called DOMpro that predicts protein domains using a combination of evolutionary information in the form of profiles and predicted secondary structure and relative solvent accessibility. DOMpro is trained and tested on a curated dataset derived from the CATH datab...
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ژورنال
عنوان ژورنال: Systematic Biology
سال: 2010
ISSN: 1076-836X,1063-5157
DOI: 10.1093/sysbio/syq002