Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 97

1.

Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization.

Ge Y, Voelz VA.

J Phys Chem B. 2018 May 31;122(21):5610-5622. doi: 10.1021/acs.jpcb.7b11871. Epub 2018 Mar 23.

PMID:
29518328
2.

A Maximum-Likelihood Approach to Force-Field Calibration.

Zaborowski B, Jagieła D, Czaplewski C, Hałabis A, Lewandowska A, Żmudzińska W, Ołdziej S, Karczyńska A, Omieczynski C, Wirecki T, Liwo A.

J Chem Inf Model. 2015 Sep 28;55(9):2050-70. doi: 10.1021/acs.jcim.5b00395. Epub 2015 Aug 20.

PMID:
26263302
3.

Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides.

Tran TT, Nguyen PH, Derreumaux P.

J Chem Phys. 2016 May 28;144(20):205103. doi: 10.1063/1.4951739.

PMID:
27250331
4.
5.

Conformational state-specific free energy differences by one-step perturbation: protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields.

Lin Z, Van Gunsteren WF, Liu H.

J Comput Chem. 2011 Jul 30;32(10):2290-7. doi: 10.1002/jcc.21818. Epub 2011 May 3.

PMID:
21541965
6.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
7.

Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme.

Soares TA, Daura X, Oostenbrink C, Smith LJ, van Gunsteren WF.

J Biomol NMR. 2004 Dec;30(4):407-22.

PMID:
15630561
8.
9.

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.

Ditzler MA, Otyepka M, Sponer J, Walter NG.

Acc Chem Res. 2010 Jan 19;43(1):40-7. doi: 10.1021/ar900093g.

10.
11.

A hierarchical Bayesian framework for force field selection in molecular dynamics simulations.

Wu S, Angelikopoulos P, Papadimitriou C, Moser R, Koumoutsakos P.

Philos Trans A Math Phys Eng Sci. 2016 Feb 13;374(2060). pii: 20150032. doi: 10.1098/rsta.2015.0032.

12.

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

Frembgen-Kesner T, Andrews CT, Li S, Ngo NA, Shubert SA, Jain A, Olayiwola OJ, Weishaar MR, Elcock AH.

J Chem Theory Comput. 2015 May 12;11(5):2341-54. doi: 10.1021/acs.jctc.5b00038. Epub 2015 Apr 30.

13.

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K.

Sci Adv. 2018 May 18;4(5):eaar8521. doi: 10.1126/sciadv.aar8521. eCollection 2018 May.

14.

Refinement of the application of the GROMOS 54A7 force field to β-peptides.

Lin Z, van Gunsteren WF.

J Comput Chem. 2013 Dec 15;34(32):2796-805. doi: 10.1002/jcc.23459. Epub 2013 Oct 7.

PMID:
24122968
15.

Bayesian parameter inference and model selection by population annealing in systems biology.

Murakami Y.

PLoS One. 2014 Aug 4;9(8):e104057. doi: 10.1371/journal.pone.0104057. eCollection 2014.

16.

PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification.

Han W, Wan CK, Jiang F, Wu YD.

J Chem Theory Comput. 2010 Nov 9;6(11):3373-89. doi: 10.1021/ct1003127.

PMID:
26617092
17.
18.

Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space.

Liu Z, Ensing B, Moore PB.

J Chem Theory Comput. 2011 Feb 8;7(2):402-19. doi: 10.1021/ct100395n. Epub 2010 Dec 29.

PMID:
26596162
19.

Sparse estimation for structural variability.

Hosur R, Singh R, Berger B.

Algorithms Mol Biol. 2011 Apr 19;6:12. doi: 10.1186/1748-7188-6-12.

20.

Fast and robust Block-Sparse Bayesian learning for EEG source imaging.

Ojeda A, Kreutz-Delgado K, Mullen T.

Neuroimage. 2018 Jul 1;174:449-462. doi: 10.1016/j.neuroimage.2018.03.048. Epub 2018 Mar 27.

PMID:
29596978

Supplemental Content

Support Center