Abstract
We introduce "library-based Monte Carlo" (LBMC) simulation, which performs Boltzmann sampling of molecular systems based on precalculated statistical libraries of molecular-fragment configurations, energies, and interactions. The library for each fragment can be Boltzmann distributed and thus account for all correlations internal to the fragment. LBMC can be applied to both atomistic and coarse-grained models, as we demonstrate in this "proof-of-principle" report. We first verify the approach in a toy model and in implicitly solvated all-atom polyalanine systems. We next study five proteins, up to 309 residues in size. On the basis of atomistic equilibrium libraries of peptide-plane configurations, the proteins are modeled with fully atomistic backbones and simplified Gō-like interactions among residues. We show that full equilibrium sampling can be obtained in days to weeks on a single processor, suggesting that more accurate models are well within reach. For the future, LBMC provides a convenient platform for constructing adjustable or mixed-resolution models: the configurations of all atoms can be stored at no run-time cost, while an arbitrary subset of interactions is "turned on".
| Original language | English (US) |
|---|---|
| Pages (from-to) | 10891-10904 |
| Number of pages | 14 |
| Journal | Journal of Physical Chemistry B |
| Volume | 113 |
| Issue number | 31 |
| DOIs | |
| State | Published - Aug 6 2009 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Physical and Theoretical Chemistry
- Surfaces, Coatings and Films
- Materials Chemistry
Cite this
General library-based monte carlo technique enables equilibrium sampling of semi-atomistic protein models. / Mamonov, Artem B.; Bhatt, Divesh; Cashman, Derek J.; Ding, Ying; Zuckerman, Daniel.
In: Journal of Physical Chemistry B, Vol. 113, No. 31, 06.08.2009, p. 10891-10904.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - General library-based monte carlo technique enables equilibrium sampling of semi-atomistic protein models
AU - Mamonov, Artem B.
AU - Bhatt, Divesh
AU - Cashman, Derek J.
AU - Ding, Ying
AU - Zuckerman, Daniel
PY - 2009/8/6
Y1 - 2009/8/6
N2 - We introduce "library-based Monte Carlo" (LBMC) simulation, which performs Boltzmann sampling of molecular systems based on precalculated statistical libraries of molecular-fragment configurations, energies, and interactions. The library for each fragment can be Boltzmann distributed and thus account for all correlations internal to the fragment. LBMC can be applied to both atomistic and coarse-grained models, as we demonstrate in this "proof-of-principle" report. We first verify the approach in a toy model and in implicitly solvated all-atom polyalanine systems. We next study five proteins, up to 309 residues in size. On the basis of atomistic equilibrium libraries of peptide-plane configurations, the proteins are modeled with fully atomistic backbones and simplified Gō-like interactions among residues. We show that full equilibrium sampling can be obtained in days to weeks on a single processor, suggesting that more accurate models are well within reach. For the future, LBMC provides a convenient platform for constructing adjustable or mixed-resolution models: the configurations of all atoms can be stored at no run-time cost, while an arbitrary subset of interactions is "turned on".
AB - We introduce "library-based Monte Carlo" (LBMC) simulation, which performs Boltzmann sampling of molecular systems based on precalculated statistical libraries of molecular-fragment configurations, energies, and interactions. The library for each fragment can be Boltzmann distributed and thus account for all correlations internal to the fragment. LBMC can be applied to both atomistic and coarse-grained models, as we demonstrate in this "proof-of-principle" report. We first verify the approach in a toy model and in implicitly solvated all-atom polyalanine systems. We next study five proteins, up to 309 residues in size. On the basis of atomistic equilibrium libraries of peptide-plane configurations, the proteins are modeled with fully atomistic backbones and simplified Gō-like interactions among residues. We show that full equilibrium sampling can be obtained in days to weeks on a single processor, suggesting that more accurate models are well within reach. For the future, LBMC provides a convenient platform for constructing adjustable or mixed-resolution models: the configurations of all atoms can be stored at no run-time cost, while an arbitrary subset of interactions is "turned on".
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UR - http://www.scopus.com/inward/citedby.url?scp=68149131990&partnerID=8YFLogxK
U2 - 10.1021/jp901322v
DO - 10.1021/jp901322v
M3 - Article
C2 - 19594147
AN - SCOPUS:68149131990
VL - 113
SP - 10891
EP - 10904
JO - Journal of Physical Chemistry B Materials
JF - Journal of Physical Chemistry B Materials
SN - 1520-6106
IS - 31
ER -