155 related articles for article (PubMed ID: 33629765)
1. Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning.
Jin Y; Johannissen LO; Hay S
Proteins; 2021 Feb; ():. PubMed ID: 33629765
[TBL] [Abstract][Full Text] [Related]
2. Enhancing Conformational Sampling for Intrinsically Disordered and Ordered Proteins by Variational Autoencoder.
Zhu JJ; Zhang NJ; Wei T; Chen HF
Int J Mol Sci; 2023 Apr; 24(8):. PubMed ID: 37108059
[TBL] [Abstract][Full Text] [Related]
3. Machine Learning Generation of Dynamic Protein Conformational Ensembles.
Zheng LE; Barethiya S; Nordquist E; Chen J
Molecules; 2023 May; 28(10):. PubMed ID: 37241789
[TBL] [Abstract][Full Text] [Related]
4. Explore Protein Conformational Space With Variational Autoencoder.
Tian H; Jiang X; Trozzi F; Xiao S; Larson EC; Tao P
Front Mol Biosci; 2021; 8():781635. PubMed ID: 34869602
[TBL] [Abstract][Full Text] [Related]
5. Assessments of Variational Autoencoder in Protein Conformation Exploration.
Xiao S; Song Z; Tian H; Tao P
J Comput Biophys Chem; 2023 Jun; 22(4):489-501. PubMed ID: 38826699
[TBL] [Abstract][Full Text] [Related]
6. Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling.
Zhu J; Li Z; Tong H; Lu Z; Zhang N; Wei T; Chen HF
Brief Bioinform; 2023 Nov; 25(1):. PubMed ID: 38018910
[TBL] [Abstract][Full Text] [Related]
7. Computational methods for exploring protein conformations.
Allison JR
Biochem Soc Trans; 2020 Aug; 48(4):1707-1724. PubMed ID: 32756904
[TBL] [Abstract][Full Text] [Related]
8. LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories.
Tian H; Jiang X; Xiao S; La Force H; Larson EC; Tao P
J Chem Inf Model; 2023 Jan; 63(1):67-75. PubMed ID: 36472885
[TBL] [Abstract][Full Text] [Related]
9. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.
Kandel S; Salomon-Ferrer R; Larsen AB; Jain A; Vaidehi N
J Chem Phys; 2016 Jan; 144(4):044112. PubMed ID: 26827207
[TBL] [Abstract][Full Text] [Related]
10. Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes.
Shamsi Z; Cheng KJ; Shukla D
J Phys Chem B; 2018 Sep; 122(35):8386-8395. PubMed ID: 30126271
[TBL] [Abstract][Full Text] [Related]
11. Mapping conformational dynamics of proteins using torsional dynamics simulations.
Gangupomu VK; Wagner JR; Park IH; Jain A; Vaidehi N
Biophys J; 2013 May; 104(9):1999-2008. PubMed ID: 23663843
[TBL] [Abstract][Full Text] [Related]
12. Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics.
Yasuda T; Shigeta Y; Harada R
J Chem Inf Model; 2020 Aug; 60(8):4021-4029. PubMed ID: 32786508
[TBL] [Abstract][Full Text] [Related]
13. Identifying multiple active conformations in the G protein-coupled receptor activation landscape using computational methods.
Dong SS; Goddard WA; Abrol R
Methods Cell Biol; 2017; 142():173-186. PubMed ID: 28964335
[TBL] [Abstract][Full Text] [Related]
14. Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations.
Srivastava A; Bala S; Motomura H; Kohda D; Tama F; Miyashita O
Biochim Biophys Acta Gen Subj; 2020 Feb; 1864(2):129417. PubMed ID: 31445064
[TBL] [Abstract][Full Text] [Related]
15. Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.
Ikebe J; Umezawa K; Higo J
Biophys Rev; 2016 Mar; 8(1):45-62. PubMed ID: 28510144
[TBL] [Abstract][Full Text] [Related]
16. Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.
Ditzler MA; Otyepka M; Sponer J; Walter NG
Acc Chem Res; 2010 Jan; 43(1):40-7. PubMed ID: 19754142
[TBL] [Abstract][Full Text] [Related]
17. Direct generation of protein conformational ensembles via machine learning.
Janson G; Valdes-Garcia G; Heo L; Feig M
Nat Commun; 2023 Feb; 14(1):774. PubMed ID: 36774359
[TBL] [Abstract][Full Text] [Related]
18. CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space.
Shkurti A; Styliari ID; Balasubramanian V; Bethune I; Pedebos C; Jha S; Laughton CA
J Chem Theory Comput; 2019 Apr; 15(4):2587-2596. PubMed ID: 30620585
[TBL] [Abstract][Full Text] [Related]
19. 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]
20. Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer.
Yan S; Peck JM; Ilgu M; Nilsen-Hamilton M; Lamm MH
ACS Omega; 2020 Aug; 5(32):20187-20201. PubMed ID: 32832772
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]