473 related articles for article (PubMed ID: 26616065)
1. Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries.
Hansen HS; Hünenberger PH
J Chem Theory Comput; 2010 Sep; 6(9):2622-46. PubMed ID: 26616065
[TBL] [Abstract][Full Text] [Related]
2. Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling.
Hansen HS; Daura X; Hünenberger PH
J Chem Theory Comput; 2010 Sep; 6(9):2598-621. PubMed ID: 26616064
[TBL] [Abstract][Full Text] [Related]
3. Using the local elevation method to construct optimized umbrella sampling potentials: calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water.
Hansen HS; Hünenberger PH
J Comput Chem; 2010 Jan; 31(1):1-23. PubMed ID: 19412904
[TBL] [Abstract][Full Text] [Related]
4. On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical conformations of decaalanine in water.
Bieler NS; Hünenberger PH
J Chem Phys; 2015 Apr; 142(16):165102. PubMed ID: 25933791
[TBL] [Abstract][Full Text] [Related]
5. Local Elevation Umbrella Sampling Applied to the Calculation of Alchemical Free-Energy Changes via λ-Dynamics: The λ-LEUS Scheme.
Bieler NS; Häuselmann R; Hünenberger PH
J Chem Theory Comput; 2014 Aug; 10(8):3006-22. PubMed ID: 26588272
[TBL] [Abstract][Full Text] [Related]
6. Communication: estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth.
Bieler NS; Hünenberger PH
J Chem Phys; 2014 Nov; 141(20):201101. PubMed ID: 25429926
[TBL] [Abstract][Full Text] [Related]
7. On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, α-, and π-Helices.
Lin Z; Liu H; Riniker S; van Gunsteren WF
J Chem Theory Comput; 2011 Dec; 7(12):3884-97. PubMed ID: 26598335
[TBL] [Abstract][Full Text] [Related]
8. Multistate λ-local-elevation umbrella-sampling (MS-λ-LEUS): method and application to the complexation of cations by crown ethers.
Bieler NS; Tschopp JP; Hünenberger PH
J Chem Theory Comput; 2015 Jun; 11(6):2575-88. PubMed ID: 26575556
[TBL] [Abstract][Full Text] [Related]
9. Free-energy differences between states with different conformational ensembles.
Garate JA; Oostenbrink C
J Comput Chem; 2013 Jun; 34(16):1398-408. PubMed ID: 23526629
[TBL] [Abstract][Full Text] [Related]
10. Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI versus λ-LEUS.
Bieler NS; Hünenberger PH
J Comput Chem; 2015 Aug; 36(22):1686-97. PubMed ID: 26154740
[TBL] [Abstract][Full Text] [Related]
11. Alchemical Free-Energy Calculations by Multiple-Replica λ-Dynamics: The Conveyor Belt Thermodynamic Integration Scheme.
Hahn DF; Hünenberger PH
J Chem Theory Comput; 2019 Apr; 15(4):2392-2419. PubMed ID: 30821973
[TBL] [Abstract][Full Text] [Related]
12. Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.
Perić-Hassler L; Hansen HS; Baron R; Hünenberger PH
Carbohydr Res; 2010 Aug; 345(12):1781-801. PubMed ID: 20576257
[TBL] [Abstract][Full Text] [Related]
13. Enhanced conformational sampling using enveloping distribution sampling.
Lin Z; van Gunsteren WF
J Chem Phys; 2013 Oct; 139(14):144105. PubMed ID: 24116601
[TBL] [Abstract][Full Text] [Related]
14. Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace.
Yasuda T; Morita R; Shigeta Y; Harada R
J Chem Inf Model; 2022 Dec; 62(23):6217-6227. PubMed ID: 36449380
[TBL] [Abstract][Full Text] [Related]
15. Computing Free Energy Differences of Configurational Basins.
Giovannelli E; Cardini G; Gellini C; Pietraperzia G; Chelli R
J Chem Theory Comput; 2015 Aug; 11(8):3561-71. PubMed ID: 26574441
[TBL] [Abstract][Full Text] [Related]
16. Alchemical Free Energy Differences in Flexible Molecules from Thermodynamic Integration or Free Energy Perturbation Combined with Driven Adiabatic Dynamics.
Cuendet MA; Tuckerman ME
J Chem Theory Comput; 2012 Oct; 8(10):3504-12. PubMed ID: 26592999
[TBL] [Abstract][Full Text] [Related]
17. Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics.
Awasthi S; Kapil V; Nair NN
J Comput Chem; 2016 Jun; 37(16):1413-24. PubMed ID: 27059305
[TBL] [Abstract][Full Text] [Related]
18. Determination of conformational free energies of peptides by multidimensional adaptive umbrella sampling.
Wang J; Gu Y; Liu H
J Chem Phys; 2006 Sep; 125(9):094907. PubMed ID: 16965119
[TBL] [Abstract][Full Text] [Related]
19. Using enveloping distribution sampling to compute the free enthalpy difference between right- and left-handed helices of a β-peptide in solution.
Lin Z; Timmerscheidt TA; van Gunsteren WF
J Chem Phys; 2012 Aug; 137(6):064108. PubMed ID: 22897256
[TBL] [Abstract][Full Text] [Related]
20. Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.
Yang M; Huang J; MacKerell AD
J Chem Theory Comput; 2015 Jun; 11(6):2855-67. PubMed ID: 26082676
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
