PMID- 26583735
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20151124
LR  - 20151120
IS  - 1549-9618 (Print)
IS  - 1549-9618 (Linking)
VI  - 9
IP  - 5
DP  - 2013 May 14
TI  - The Theory of Ultra-Coarse-Graining. 1. General Principles.
PG  - 2466-80
LID - 10.1021/ct4000444 [doi]
AB  - Coarse-grained (CG) models provide a computationally efficient means to study 
      biomolecular and other soft matter processes involving large numbers of atoms 
      correlated over distance scales of many covalent bond lengths and long time 
      scales. Variational methods based on information from simulations of 
      finer-grained (e.g., all-atom) models, for example the multiscale coarse-graining 
      (MS-CG) and relative entropy minimization methods, provide attractive tools for 
      the systematic development of CG models. However, these methods have important 
      drawbacks when used in the "ultra-coarse-grained" (UCG) regime, e.g., at a 
      resolution level coarser or much coarser than one amino acid residue per 
      effective CG particle in proteins. This is due to the possible existence of 
      multiple metastable states "within" the CG sites for a given UCG model 
      configuration. In this work, systematic variational UCG methods are presented 
      that are specifically designed to CG entire protein domains and subdomains into 
      single effective CG particles. This is accomplished by augmenting existing 
      effective particle CG schemes to allow for discrete state transitions and 
      configuration-dependent resolution. Additionally, certain conclusions of this 
      work connect back to single-state force matching and open up new avenues for 
      method development in that area. These results provide a formal statistical 
      mechanical basis for UCG methods related to force matching and relative entropy 
      CG methods and suggest practical algorithms for constructing optimal approximate 
      UCG models from fine-grained simulation data.
FAU - Dama, James F
AU  - Dama JF
AD  - Department of Chemistry and Institute for Biophysical Dynamics, double daggerComputation 
      Institute,  section signJames Franck Institute,  parallelDepartment of Mathematics,  perpendicularDepartment of 
      Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 
      60637, United States.
FAU - Sinitskiy, Anton V
AU  - Sinitskiy AV
AD  - Department of Chemistry and Institute for Biophysical Dynamics, double daggerComputation 
      Institute,  section signJames Franck Institute,  parallelDepartment of Mathematics,  perpendicularDepartment of 
      Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 
      60637, United States.
FAU - McCullagh, Martin
AU  - McCullagh M
AD  - Department of Chemistry and Institute for Biophysical Dynamics, double daggerComputation 
      Institute,  section signJames Franck Institute,  parallelDepartment of Mathematics,  perpendicularDepartment of 
      Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 
      60637, United States.
FAU - Weare, Jonathan
AU  - Weare J
AD  - Department of Chemistry and Institute for Biophysical Dynamics, double daggerComputation 
      Institute,  section signJames Franck Institute,  parallelDepartment of Mathematics,  perpendicularDepartment of 
      Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 
      60637, United States.
FAU - Roux, Benoit
AU  - Roux B
AD  - Department of Chemistry and Institute for Biophysical Dynamics, double daggerComputation 
      Institute,  section signJames Franck Institute,  parallelDepartment of Mathematics,  perpendicularDepartment of 
      Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 
      60637, United States.
FAU - Dinner, Aaron R
AU  - Dinner AR
AD  - Department of Chemistry and Institute for Biophysical Dynamics, double daggerComputation 
      Institute,  section signJames Franck Institute,  parallelDepartment of Mathematics,  perpendicularDepartment of 
      Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 
      60637, United States.
FAU - Voth, Gregory A
AU  - Voth GA
AD  - Department of Chemistry and Institute for Biophysical Dynamics, double daggerComputation 
      Institute,  section signJames Franck Institute,  parallelDepartment of Mathematics,  perpendicularDepartment of 
      Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 
      60637, United States.
LA  - eng
PT  - Journal Article
DEP - 20130410
PL  - United States
TA  - J Chem Theory Comput
JT  - Journal of chemical theory and computation
JID - 101232704
EDAT- 2013/05/14 00:00
MHDA- 2013/05/14 00:01
CRDT- 2015/11/20 06:00
PHST- 2015/11/20 06:00 [entrez]
PHST- 2013/05/14 00:00 [pubmed]
PHST- 2013/05/14 00:01 [medline]
AID - 10.1021/ct4000444 [doi]
PST - ppublish
SO  - J Chem Theory Comput. 2013 May 14;9(5):2466-80. doi: 10.1021/ct4000444. Epub 2013 
      Apr 10.