The Roles of Entropy and Kinetics in Structure Prediction
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{"title"=>"The roles of entropy and kinetics in structure prediction", "type"=>"journal", "authors"=>[{"first_name"=>"Gregory R.", "last_name"=>"Bowman", "scopus_author_id"=>"24334008700"}, {"first_name"=>"Vijay S.", "last_name"=>"Pande", "scopus_author_id"=>"7004966384"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-67649203376", "sgr"=>"67649203376", "pui"=>"354774207", "pmid"=>"19513117", "doi"=>"10.1371/journal.pone.0005840"}, "id"=>"4d8199ce-441d-3e7f-a472-d5d5f1fcba34", "abstract"=>"BACKGROUND: Here we continue our efforts to use methods developed in the folding mechanism community to both better understand and improve structure prediction. Our previous work demonstrated that Rosetta's coarse-grained potentials may actually impede accurate structure prediction at full-atom resolution. Based on this work we postulated that it may be time to work completely at full-atom resolution but that doing so may require more careful attention to the kinetics of convergence.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: To explore the possibility of working entirely at full-atom resolution, we apply enhanced sampling algorithms and the free energy theory developed in the folding mechanism community to full-atom protein structure prediction with the prominent Rosetta package. We find that Rosetta's full-atom scoring function is indeed able to recognize diverse protein native states and that there is a strong correlation between score and Calpha RMSD to the native state. However, we also show that there is a huge entropic barrier to folding under this potential and the kinetics of folding are extremely slow. We then exploit this new understanding to suggest ways to improve structure prediction.\\n\\nCONCLUSIONS/SIGNIFICANCE: Based on this work we hypothesize that structure prediction may be improved by taking a more physical approach, i.e. considering the nature of the model thermodynamics and kinetics which result from structure prediction simulations.", "link"=>"http://www.mendeley.com/research/roles-entropy-kinetics-structure-prediction", "reader_count"=>55, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>20, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>2, "Student > Master"=>2, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>20, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>2, "Student > Master"=>2, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Mathematics"=>2, "Agricultural and Biological Sciences"=>24, "Philosophy"=>1, "Neuroscience"=>1, "Arts and Humanities"=>1, "Physics and Astronomy"=>3, "Chemistry"=>11, "Social Sciences"=>1, "Computer Science"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>11}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>24}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Argentina"=>2, "United States"=>3, "Germany"=>1, "Spain"=>2}, "group_count"=>4}

Scopus | Further Information

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Figshare

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Relative Metric

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