279 related articles for article (PubMed ID: 33078950)
1. Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins.
Tang WS; Fawzi NL; Mittal J
J Phys Chem B; 2020 Oct; 124(43):9505-9512. PubMed ID: 33078950
[TBL] [Abstract][Full Text] [Related]
2. Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles.
Chan-Yao-Chong M; Durand D; Ha-Duong T
J Chem Inf Model; 2019 May; 59(5):1743-1758. PubMed ID: 30840442
[TBL] [Abstract][Full Text] [Related]
3. Comparison and Evaluation of Force Fields for Intrinsically Disordered Proteins.
Rahman MU; Rehman AU; Liu H; Chen HF
J Chem Inf Model; 2020 Oct; 60(10):4912-4923. PubMed ID: 32816485
[TBL] [Abstract][Full Text] [Related]
4. Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins.
Yang S; Liu H; Zhang Y; Lu H; Chen H
J Chem Inf Model; 2019 Nov; 59(11):4793-4805. PubMed ID: 31613621
[TBL] [Abstract][Full Text] [Related]
5. Residual Structures and Transient Long-Range Interactions of p53 Transactivation Domain: Assessment of Explicit Solvent Protein Force Fields.
Liu X; Chen J
J Chem Theory Comput; 2019 Aug; 15(8):4708-4720. PubMed ID: 31241933
[TBL] [Abstract][Full Text] [Related]
6. Development of Charge-Augmented Three-Point Water Model (CAIPi3P) for Accurate Simulations of Intrinsically Disordered Proteins.
de Souza JV; Zariquiey FS; Bronowska AK
Int J Mol Sci; 2020 Aug; 21(17):. PubMed ID: 32859072
[TBL] [Abstract][Full Text] [Related]
7. Intrinsically disordered protein-specific force field CHARMM36IDPSFF.
Liu H; Song D; Lu H; Luo R; Chen HF
Chem Biol Drug Des; 2018 Oct; 92(4):1722-1735. PubMed ID: 29808548
[TBL] [Abstract][Full Text] [Related]
8. The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins.
Song D; Luo R; Chen HF
J Chem Inf Model; 2017 May; 57(5):1166-1178. PubMed ID: 28448138
[TBL] [Abstract][Full Text] [Related]
9. Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields.
Gopal SM; Wingbermühle S; Schnatwinkel J; Juber S; Herrmann C; Schäfer LV
J Phys Chem B; 2021 Jan; 125(1):24-35. PubMed ID: 33382616
[TBL] [Abstract][Full Text] [Related]
10. Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins.
Liu H; Song D; Zhang Y; Yang S; Luo R; Chen HF
Phys Chem Chem Phys; 2019 Oct; 21(39):21918-21931. PubMed ID: 31552948
[TBL] [Abstract][Full Text] [Related]
11. Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations.
Shrestha UR; Smith JC; Petridis L
Commun Biol; 2021 Feb; 4(1):243. PubMed ID: 33623120
[TBL] [Abstract][Full Text] [Related]
12. Developing a molecular dynamics force field for both folded and disordered protein states.
Robustelli P; Piana S; Shaw DE
Proc Natl Acad Sci U S A; 2018 May; 115(21):E4758-E4766. PubMed ID: 29735687
[TBL] [Abstract][Full Text] [Related]
13. Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment.
Rauscher S; Gapsys V; Gajda MJ; Zweckstetter M; de Groot BL; Grubmüller H
J Chem Theory Comput; 2015 Nov; 11(11):5513-24. PubMed ID: 26574339
[TBL] [Abstract][Full Text] [Related]
14. Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing.
Chen SH; Weiss KL; Stanley C; Bhowmik D
Protein Sci; 2023 Oct; 32(10):e4772. PubMed ID: 37646172
[TBL] [Abstract][Full Text] [Related]
15. Balanced Amino-Acid-Specific Molecular Dynamics Force Field for the Realistic Simulation of Both Folded and Disordered Proteins.
Yu L; Li DW; Brüschweiler R
J Chem Theory Comput; 2020 Feb; 16(2):1311-1318. PubMed ID: 31877033
[TBL] [Abstract][Full Text] [Related]
16. Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins.
Song D; Liu H; Luo R; Chen HF
J Chem Inf Model; 2020 Apr; 60(4):2257-2267. PubMed ID: 32227937
[TBL] [Abstract][Full Text] [Related]
17. Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties.
Zerze GH; Zheng W; Best RB; Mittal J
J Phys Chem Lett; 2019 May; 10(9):2227-2234. PubMed ID: 30990694
[TBL] [Abstract][Full Text] [Related]
18. Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions.
Fatafta H; Samantray S; Sayyed-Ahmad A; Coskuner-Weber O; Strodel B
Prog Mol Biol Transl Sci; 2021; 183():135-185. PubMed ID: 34656328
[TBL] [Abstract][Full Text] [Related]
19. Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions.
Zapletal V; Mládek A; Melková K; Louša P; Nomilner E; Jaseňáková Z; Kubáň V; Makovická M; Laníková A; Žídek L; Hritz J
Biophys J; 2020 Apr; 118(7):1621-1633. PubMed ID: 32367806
[TBL] [Abstract][Full Text] [Related]
20. Systematic Differences between Current Molecular Dynamics Force Fields To Represent Local Properties of Intrinsically Disordered Proteins.
Yu L; Li DW; Brüschweiler R
J Phys Chem B; 2021 Jan; 125(3):798-804. PubMed ID: 33444020
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
