These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
4. Coarse-grained molecular simulations of large biomolecules. Takada S Curr Opin Struct Biol; 2012 Apr; 22(2):130-7. PubMed ID: 22365574 [TBL] [Abstract][Full Text] [Related]
5. The CUMULUS coarse graining method: transferable potentials for water and solutes. van Hoof B; Markvoort AJ; van Santen RA; Hilbers PA J Phys Chem B; 2011 Aug; 115(33):10001-12. PubMed ID: 21740053 [TBL] [Abstract][Full Text] [Related]
6. Van der Waals Perspective on Coarse-Graining: Progress toward Solving Representability and Transferability Problems. Dunn NJ; Foley TT; Noid WG Acc Chem Res; 2016 Dec; 49(12):2832-2840. PubMed ID: 27993007 [TBL] [Abstract][Full Text] [Related]
7. Multiscale simulation of small peptides: consistent conformational sampling in atomistic and coarse-grained models. Bezkorovaynaya O; Lukyanov A; Kremer K; Peter C J Comput Chem; 2012 Apr; 33(9):937-49. PubMed ID: 22298285 [TBL] [Abstract][Full Text] [Related]
8. Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models. Chan HS; Zhang Z; Wallin S; Liu Z Annu Rev Phys Chem; 2011; 62():301-26. PubMed ID: 21453060 [TBL] [Abstract][Full Text] [Related]
9. A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations. Riniker S; van Gunsteren WF J Chem Phys; 2011 Feb; 134(8):084110. PubMed ID: 21361530 [TBL] [Abstract][Full Text] [Related]
10. Systematic methods for defining coarse-grained maps in large biomolecules. Zhang Z Adv Exp Med Biol; 2015; 827():33-48. PubMed ID: 25387958 [TBL] [Abstract][Full Text] [Related]
11. Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. Kamerlin SC; Vicatos S; Dryga A; Warshel A Annu Rev Phys Chem; 2011; 62():41-64. PubMed ID: 21034218 [TBL] [Abstract][Full Text] [Related]
12. Advances in coarse-grained modeling of macromolecular complexes. Pak AJ; Voth GA Curr Opin Struct Biol; 2018 Oct; 52():119-126. PubMed ID: 30508766 [TBL] [Abstract][Full Text] [Related]
13. Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization. Li M; Zhang JZ; Xia F J Chem Theory Comput; 2016 Apr; 12(4):2091-100. PubMed ID: 26930392 [TBL] [Abstract][Full Text] [Related]
14. Coarse-grained models: getting more with less. Rader AJ Curr Opin Pharmacol; 2010 Dec; 10(6):753-9. PubMed ID: 20888293 [TBL] [Abstract][Full Text] [Related]
15. The multiscale coarse-graining method. VIII. Multiresolution hierarchical basis functions and basis function selection in the construction of coarse-grained force fields. Das A; Andersen HC J Chem Phys; 2012 May; 136(19):194113. PubMed ID: 22612086 [TBL] [Abstract][Full Text] [Related]
16. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Rzepiela AJ; Louhivuori M; Peter C; Marrink SJ Phys Chem Chem Phys; 2011 Jun; 13(22):10437-48. PubMed ID: 21494747 [TBL] [Abstract][Full Text] [Related]
17. Exploration of transferability in multiscale coarse-grained peptide models. Thorpe IF; Goldenberg DP; Voth GA J Phys Chem B; 2011 Oct; 115(41):11911-26. PubMed ID: 21905717 [TBL] [Abstract][Full Text] [Related]
18. Optimal number of coarse-grained sites in different components of large biomolecular complexes. Sinitskiy AV; Saunders MG; Voth GA J Phys Chem B; 2012 Jul; 116(29):8363-74. PubMed ID: 22276676 [TBL] [Abstract][Full Text] [Related]
19. Rigorous Progress in Coarse-Graining. Noid WG; Szukalo RJ; Kidder KM; Lesniewski MC Annu Rev Phys Chem; 2024 Jun; 75(1):21-45. PubMed ID: 38941523 [TBL] [Abstract][Full Text] [Related]