119 related articles for article (PubMed ID: 36959445)
1. 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]
2. Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods.
McGuffin LJ; Shuid AN; Kempster R; Maghrabi AHA; Nealon JO; Salehe BR; Atkins JD; Roche DB
Proteins; 2018 Mar; 86 Suppl 1():335-344. PubMed ID: 28748648
[TBL] [Abstract][Full Text] [Related]
3. Methods for the Refinement of Protein Structure 3D Models.
Adiyaman R; McGuffin LJ
Int J Mol Sci; 2019 May; 20(9):. PubMed ID: 31075942
[TBL] [Abstract][Full Text] [Related]
4. ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts.
Adiyaman R; McGuffin LJ
Nucleic Acids Res; 2021 Jul; 49(W1):W589-W596. PubMed ID: 34009387
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. 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]
7. 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]
8. 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]
9. 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]
10. Physics-based protein structure refinement in the era of artificial intelligence.
Heo L; Janson G; Feig M
Proteins; 2021 Dec; 89(12):1870-1887. PubMed ID: 34156124
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates.
Shuid AN; Kempster R; McGuffin LJ
Nucleic Acids Res; 2017 Jul; 45(W1):W422-W428. PubMed ID: 28402475
[TBL] [Abstract][Full Text] [Related]
13. Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment.
Lee GR; Heo L; Seok C
Proteins; 2018 Mar; 86 Suppl 1():168-176. PubMed ID: 29044810
[TBL] [Abstract][Full Text] [Related]
14. 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]
15. 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]
16. Evaluation of model refinement in CASP13.
Read RJ; Sammito MD; Kryshtafovych A; Croll TI
Proteins; 2019 Dec; 87(12):1249-1262. PubMed ID: 31365160
[TBL] [Abstract][Full Text] [Related]
17. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.
Xu D; Zhang J; Roy A; Zhang Y
Proteins; 2011; 79 Suppl 10(Suppl 10):147-60. PubMed ID: 22069036
[TBL] [Abstract][Full Text] [Related]
18. Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling.
Zhang J; Liang Y; Zhang Y
Structure; 2011 Dec; 19(12):1784-95. PubMed ID: 22153501
[TBL] [Abstract][Full Text] [Related]
19. 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]
20. refineD: improved protein structure refinement using machine learning based restrained relaxation.
Bhattacharya D
Bioinformatics; 2019 Sep; 35(18):3320-3328. PubMed ID: 30759180
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]