100 related articles for article (PubMed ID: 28800396)
1. A Simple and Efficient Protein Structure Refinement Method.
Cheng Q; Joung I; Lee J
J Chem Theory Comput; 2017 Oct; 13(10):5146-5162. PubMed ID: 28800396
[TBL] [Abstract][Full Text] [Related]
2. Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment.
Khoury GA; Smadbeck J; Kieslich CA; Koskosidis AJ; Guzman YA; Tamamis P; Floudas CA
Proteins; 2017 Jun; 85(6):1078-1098. PubMed ID: 28241391
[TBL] [Abstract][Full Text] [Related]
3. Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent.
Terashi G; Kihara D
Proteins; 2018 Mar; 86 Suppl 1(Suppl 1):189-201. PubMed ID: 28833585
[TBL] [Abstract][Full Text] [Related]
4. Protein structure modeling and refinement by global optimization in CASP12.
Hong SH; Joung I; Flores-Canales JC; Manavalan B; Cheng Q; Heo S; Kim JY; Lee SY; Nam M; Joo K; Lee IH; Lee SJ; Lee J
Proteins; 2018 Mar; 86 Suppl 1():122-135. PubMed ID: 29159837
[TBL] [Abstract][Full Text] [Related]
5. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.
Raval A; Piana S; Eastwood MP; Dror RO; Shaw DE
Proteins; 2012 Aug; 80(8):2071-9. PubMed ID: 22513870
[TBL] [Abstract][Full Text] [Related]
6. Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging.
Mirjalili V; Noyes K; Feig M
Proteins; 2014 Feb; 82 Suppl 2(0 2):196-207. PubMed ID: 23737254
[TBL] [Abstract][Full Text] [Related]
7. Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy.
Adiyaman R; McGuffin LJ
Methods Mol Biol; 2023; 2627():119-140. PubMed ID: 36959445
[TBL] [Abstract][Full Text] [Related]
8. Significant Refinement of Protein Structure Models Using a Residue-Specific Force Field.
Xun S; Jiang F; Wu YD
J Chem Theory Comput; 2015 Apr; 11(4):1949-56. PubMed ID: 26574396
[TBL] [Abstract][Full Text] [Related]
9. Protein structure refinement of CASP target proteins using GNEIMO torsional dynamics method.
Larsen AB; Wagner JR; Jain A; Vaidehi N
J Chem Inf Model; 2014 Feb; 54(2):508-17. PubMed ID: 24397429
[TBL] [Abstract][Full Text] [Related]
10. Protein structure refinement via molecular-dynamics simulations: What works and what does not?
Feig M; Mirjalili V
Proteins; 2016 Sep; 84 Suppl 1(Suppl 1):282-92. PubMed ID: 26234208
[TBL] [Abstract][Full Text] [Related]
11. Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field.
Mozolewska MA; Krupa P; Zaborowski B; Liwo A; Lee J; Joo K; Czaplewski C
J Chem Inf Model; 2016 Nov; 56(11):2263-2279. PubMed ID: 27749055
[TBL] [Abstract][Full Text] [Related]
12. Driven to near-experimental accuracy by refinement via molecular dynamics simulations.
Heo L; Arbour CF; Feig M
Proteins; 2019 Dec; 87(12):1263-1275. PubMed ID: 31197841
[TBL] [Abstract][Full Text] [Related]
13. Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.
Raval A; Piana S; Eastwood MP; Shaw DE
Protein Sci; 2016 Jan; 25(1):19-29. PubMed ID: 26266489
[TBL] [Abstract][Full Text] [Related]
14. Protein structure refinement with adaptively restrained homologous replicas.
Della Corte D; Wildberg A; Schröder GF
Proteins; 2016 Sep; 84 Suppl 1():302-13. PubMed ID: 26441154
[TBL] [Abstract][Full Text] [Related]
15. Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis.
Flohil JA; Vriend G; Berendsen HJ
Proteins; 2002 Sep; 48(4):593-604. PubMed ID: 12211026
[TBL] [Abstract][Full Text] [Related]
16. Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines.
Khoury GA; Tamamis P; Pinnaduwage N; Smadbeck J; Kieslich CA; Floudas CA
Proteins; 2014 May; 82(5):794-814. PubMed ID: 24174311
[TBL] [Abstract][Full Text] [Related]
17. A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions.
Sala D; Giachetti A; Luchinat C; Rosato A
J Biomol NMR; 2016 Nov; 66(3):175-185. PubMed ID: 27771862
[TBL] [Abstract][Full Text] [Related]
18. i3Drefine software for protein 3D structure refinement and its assessment in CASP10.
Bhattacharya D; Cheng J
PLoS One; 2013; 8(7):e69648. PubMed ID: 23894517
[TBL] [Abstract][Full Text] [Related]
19. What makes it difficult to refine protein models further via molecular dynamics simulations?
Heo L; Feig M
Proteins; 2018 Mar; 86 Suppl 1(Suppl 1):177-188. PubMed ID: 28975670
[TBL] [Abstract][Full Text] [Related]
20. Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.
Feig M
J Chem Inf Model; 2016 Jul; 56(7):1304-12. PubMed ID: 27380201
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
