Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach.
We develop a general minimally coupled subspace approach (MCSA) to compute absolute entropies of macromolecules, such as proteins, from computer generated canonical ensembles. Our approach overcomes limitations of current estimates such as the quasi-harmonic approximation which neglects non-linear a...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2010-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2826394?pdf=render |
| _version_ | 1819128917313716224 |
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| author | Ulf Hensen Oliver F Lange Helmut Grubmüller |
| author_facet | Ulf Hensen Oliver F Lange Helmut Grubmüller |
| author_sort | Ulf Hensen |
| collection | DOAJ |
| description | We develop a general minimally coupled subspace approach (MCSA) to compute absolute entropies of macromolecules, such as proteins, from computer generated canonical ensembles. Our approach overcomes limitations of current estimates such as the quasi-harmonic approximation which neglects non-linear and higher-order correlations as well as multi-minima characteristics of protein energy landscapes. Here, Full Correlation Analysis, adaptive kernel density estimation, and mutual information expansions are combined and high accuracy is demonstrated for a number of test systems ranging from alkanes to a 14 residue peptide. We further computed the configurational entropy for the full 67-residue cofactor of the TATA box binding protein illustrating that MCSA yields improved results also for large macromolecular systems. |
| first_indexed | 2024-12-22T08:35:26Z |
| format | Article |
| id | doaj.art-7955e90ef6104d01b66a16344a49cd1f |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T08:35:26Z |
| publishDate | 2010-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-7955e90ef6104d01b66a16344a49cd1f2022-12-21T18:32:23ZengPublic Library of Science (PLoS)PLoS ONE1932-62032010-01-0152e917910.1371/journal.pone.0009179Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach.Ulf HensenOliver F LangeHelmut GrubmüllerWe develop a general minimally coupled subspace approach (MCSA) to compute absolute entropies of macromolecules, such as proteins, from computer generated canonical ensembles. Our approach overcomes limitations of current estimates such as the quasi-harmonic approximation which neglects non-linear and higher-order correlations as well as multi-minima characteristics of protein energy landscapes. Here, Full Correlation Analysis, adaptive kernel density estimation, and mutual information expansions are combined and high accuracy is demonstrated for a number of test systems ranging from alkanes to a 14 residue peptide. We further computed the configurational entropy for the full 67-residue cofactor of the TATA box binding protein illustrating that MCSA yields improved results also for large macromolecular systems.http://europepmc.org/articles/PMC2826394?pdf=render |
| spellingShingle | Ulf Hensen Oliver F Lange Helmut Grubmüller Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach. PLoS ONE |
| title | Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach. |
| title_full | Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach. |
| title_fullStr | Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach. |
| title_full_unstemmed | Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach. |
| title_short | Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach. |
| title_sort | estimating absolute configurational entropies of macromolecules the minimally coupled subspace approach |
| url | http://europepmc.org/articles/PMC2826394?pdf=render |
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