210 related articles for article (PubMed ID: 26677962)
1. CG2AA: backmapping protein coarse-grained structures.
Lombardi LE; Martí MA; Capece L
Bioinformatics; 2016 Apr; 32(8):1235-7. PubMed ID: 26677962
[TBL] [Abstract][Full Text] [Related]
2. Temporally Coherent Backmapping of Molecular Trajectories From Coarse-Grained to Atomistic Resolution.
Shmilovich K; Stieffenhofer M; Charron NE; Hoffmann M
J Phys Chem A; 2022 Dec; 126(48):9124-9139. PubMed ID: 36417670
[TBL] [Abstract][Full Text] [Related]
3. WATCLUST: a tool for improving the design of drugs based on protein-water interactions.
López ED; Arcon JP; Gauto DF; Petruk AA; Modenutti CP; Dumas VG; Marti MA; Turjanski AG
Bioinformatics; 2015 Nov; 31(22):3697-9. PubMed ID: 26198103
[TBL] [Abstract][Full Text] [Related]
4. Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference.
Peng J; Yuan C; Ma R; Zhang Z
J Chem Theory Comput; 2019 May; 15(5):3344-3353. PubMed ID: 30908042
[TBL] [Abstract][Full Text] [Related]
5. Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.
Wassenaar TA; Ingólfsson HI; Priess M; Marrink SJ; Schäfer LV
J Phys Chem B; 2013 Apr; 117(13):3516-30. PubMed ID: 23406326
[TBL] [Abstract][Full Text] [Related]
6. SIRAH tools: mapping, backmapping and visualization of coarse-grained models.
Machado MR; Pantano S
Bioinformatics; 2016 May; 32(10):1568-70. PubMed ID: 26773132
[TBL] [Abstract][Full Text] [Related]
7. Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein-DNA Complexes.
Shimizu M; Takada S
J Chem Theory Comput; 2018 Mar; 14(3):1682-1694. PubMed ID: 29397721
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.
May A; Pool R; van Dijk E; Bijlard J; Abeln S; Heringa J; Feenstra KA
Bioinformatics; 2014 Feb; 30(3):326-34. PubMed ID: 24273239
[TBL] [Abstract][Full Text] [Related]
10. SecStAnT: secondary structure analysis tool for data selection, statistics and models building.
Maccari G; Spampinato GL; Tozzini V
Bioinformatics; 2014 Mar; 30(5):668-74. PubMed ID: 24130306
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations.
Faustino I; Marrink SJ
Bioinformatics; 2017 Dec; 33(23):3813-3815. PubMed ID: 29036584
[TBL] [Abstract][Full Text] [Related]
13. Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy.
Li M; Teng B; Lu W; Zhang JZ
J Mol Model; 2020 Jan; 26(2):31. PubMed ID: 31965325
[TBL] [Abstract][Full Text] [Related]
14. Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.
Kar P; Feig M
J Chem Theory Comput; 2017 Nov; 13(11):5753-5765. PubMed ID: 28992696
[TBL] [Abstract][Full Text] [Related]
15. Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models.
Zhang Z; Pfaendtner J; Grafmüller A; Voth GA
Biophys J; 2009 Oct; 97(8):2327-37. PubMed ID: 19843465
[TBL] [Abstract][Full Text] [Related]
16. Reconstruction of atomistic details from coarse-grained structures.
Rzepiela AJ; Schäfer LV; Goga N; Risselada HJ; De Vries AH; Marrink SJ
J Comput Chem; 2010 Apr; 31(6):1333-43. PubMed ID: 20087907
[TBL] [Abstract][Full Text] [Related]
17. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.
Takada S; Kanada R; Tan C; Terakawa T; Li W; Kenzaki H
Acc Chem Res; 2015 Dec; 48(12):3026-35. PubMed ID: 26575522
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model.
Jamroz M; Kolinski A; Kmiecik S
Methods Mol Biol; 2014; 1137():235-50. PubMed ID: 24573485
[TBL] [Abstract][Full Text] [Related]
20. High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.
Haxton TK
J Chem Theory Comput; 2015 Mar; 11(3):1244-54. PubMed ID: 26579771
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]