The evolution of logic circuits for the purpose of protein contact map prediction
Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a nove...
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PeerJ Inc.
2017-04-01
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| Online Access: | https://peerj.com/articles/3139.pdf |
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doaj-86bd24468ef94845a14d72854b8549262020-11-24T22:26:23ZengPeerJ Inc.PeerJ2167-83592017-04-015e313910.7717/peerj.3139The evolution of logic circuits for the purpose of protein contact map predictionSamuel D. Chapman0Christoph Adami1Claus O. Wilke2Dukka B KC3Department of Comptuational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USADepartment of Microbiology and Molecular Genetics and Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USADepartment of Integrative Biology, The University of Texas at Austin, Austin, TX, USADepartment of Comptuational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USAPredicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset.https://peerj.com/articles/3139.pdfProtein contact map predictionEvolutionary computationMarkov networksMachine learningFeature selection |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Samuel D. Chapman Christoph Adami Claus O. Wilke Dukka B KC |
| spellingShingle |
Samuel D. Chapman Christoph Adami Claus O. Wilke Dukka B KC The evolution of logic circuits for the purpose of protein contact map prediction PeerJ Protein contact map prediction Evolutionary computation Markov networks Machine learning Feature selection |
| author_facet |
Samuel D. Chapman Christoph Adami Claus O. Wilke Dukka B KC |
| author_sort |
Samuel D. Chapman |
| title |
The evolution of logic circuits for the purpose of protein contact map prediction |
| title_short |
The evolution of logic circuits for the purpose of protein contact map prediction |
| title_full |
The evolution of logic circuits for the purpose of protein contact map prediction |
| title_fullStr |
The evolution of logic circuits for the purpose of protein contact map prediction |
| title_full_unstemmed |
The evolution of logic circuits for the purpose of protein contact map prediction |
| title_sort |
evolution of logic circuits for the purpose of protein contact map prediction |
| publisher |
PeerJ Inc. |
| series |
PeerJ |
| issn |
2167-8359 |
| publishDate |
2017-04-01 |
| description |
Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset. |
| topic |
Protein contact map prediction Evolutionary computation Markov networks Machine learning Feature selection |
| url |
https://peerj.com/articles/3139.pdf |
| work_keys_str_mv |
AT samueldchapman theevolutionoflogiccircuitsforthepurposeofproteincontactmapprediction AT christophadami theevolutionoflogiccircuitsforthepurposeofproteincontactmapprediction AT clausowilke theevolutionoflogiccircuitsforthepurposeofproteincontactmapprediction AT dukkabkc theevolutionoflogiccircuitsforthepurposeofproteincontactmapprediction AT samueldchapman evolutionoflogiccircuitsforthepurposeofproteincontactmapprediction AT christophadami evolutionoflogiccircuitsforthepurposeofproteincontactmapprediction AT clausowilke evolutionoflogiccircuitsforthepurposeofproteincontactmapprediction AT dukkabkc evolutionoflogiccircuitsforthepurposeofproteincontactmapprediction |
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