175 related articles for article (PubMed ID: 34685447)
21. Back-mapping based sampling: Coarse grained free energy landscapes as a guideline for atomistic exploration.
Hunkler S; Lemke T; Peter C; Kukharenko O
J Chem Phys; 2019 Oct; 151(15):154102. PubMed ID: 31640363
[TBL] [Abstract][Full Text] [Related]
22. 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]
23. The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials.
Lu L; Voth GA
J Chem Phys; 2011 Jun; 134(22):224107. PubMed ID: 21682507
[TBL] [Abstract][Full Text] [Related]
24. Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure.
Ingólfsson HI; Bhatia H; Aydin F; Oppelstrup T; López CA; Stanton LG; Carpenter TS; Wong S; Di Natale F; Zhang X; Moon JY; Stanley CB; Chavez JR; Nguyen K; Dharuman G; Burns V; Shrestha R; Goswami D; Gulten G; Van QN; Ramanathan A; Van Essen B; Hengartner NW; Stephen AG; Turbyville T; Bremer PT; Gnanakaran S; Glosli JN; Lightstone FC; Nissley DV; Streitz FH
J Chem Theory Comput; 2023 May; 19(9):2658-2675. PubMed ID: 37075065
[TBL] [Abstract][Full Text] [Related]
25. 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]
26. Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.
Moritsugu K; Terada T; Kidera A
PLoS Comput Biol; 2014 Oct; 10(10):e1003901. PubMed ID: 25340714
[TBL] [Abstract][Full Text] [Related]
27. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.
Jung J; Yagi K; Tan C; Oshima H; Mori T; Yu I; Matsunaga Y; Kobayashi C; Ito S; Ugarte La Torre D; Sugita Y
J Phys Chem B; 2024 Jun; 128(25):6028-6048. PubMed ID: 38876465
[TBL] [Abstract][Full Text] [Related]
28. Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling.
Dokainish HM; Sugita Y
Int J Mol Sci; 2020 Dec; 22(1):. PubMed ID: 33383937
[TBL] [Abstract][Full Text] [Related]
29. Multiscale Coarse-Graining of Mixed Phospholipid/Cholesterol Bilayers.
Izvekov S; Voth GA
J Chem Theory Comput; 2006 May; 2(3):637-48. PubMed ID: 26626671
[TBL] [Abstract][Full Text] [Related]
30. Coupled VAE: Improved Accuracy and Robustness of a Variational Autoencoder.
Cao S; Li J; Nelson KP; Kon MA
Entropy (Basel); 2022 Mar; 24(3):. PubMed ID: 35327933
[TBL] [Abstract][Full Text] [Related]
31. The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems.
Das A; Lu L; Andersen HC; Voth GA
J Chem Phys; 2012 May; 136(19):194115. PubMed ID: 22612088
[TBL] [Abstract][Full Text] [Related]
32. Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.
Chen Y; Roux B
J Chem Theory Comput; 2015 Aug; 11(8):3572-83. PubMed ID: 26574442
[TBL] [Abstract][Full Text] [Related]
33. Multiscale investigation of chemical interference in proteins.
Samiotakis A; Homouz D; Cheung MS
J Chem Phys; 2010 May; 132(17):175101. PubMed ID: 20459186
[TBL] [Abstract][Full Text] [Related]
34. A multiscale coarse-graining method for biomolecular systems.
Izvekov S; Voth GA
J Phys Chem B; 2005 Feb; 109(7):2469-73. PubMed ID: 16851243
[TBL] [Abstract][Full Text] [Related]
35. Disorder-to-order transition of an intrinsically disordered region of sortase revealed by multiscale enhanced sampling.
Moritsugu K; Terada T; Kidera A
J Am Chem Soc; 2012 Apr; 134(16):7094-101. PubMed ID: 22468560
[TBL] [Abstract][Full Text] [Related]
36. Crash data augmentation using variational autoencoder.
Islam Z; Abdel-Aty M; Cai Q; Yuan J
Accid Anal Prev; 2021 Mar; 151():105950. PubMed ID: 33370603
[TBL] [Abstract][Full Text] [Related]
37. Nonlinear quality-related fault detection using combined deep variational information bottleneck and variational autoencoder.
Tang P; Peng K; Dong J
ISA Trans; 2021 Aug; 114():444-454. PubMed ID: 33483094
[TBL] [Abstract][Full Text] [Related]
38. Optimization of physical quantities in the autoencoder latent space.
Park SM; Yoon HG; Lee DB; Choi JW; Kwon HY; Won C
Sci Rep; 2022 May; 12(1):9003. PubMed ID: 35637207
[TBL] [Abstract][Full Text] [Related]
39. 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]
40. Multiscale enhanced path sampling based on the Onsager-Machlup action: application to a model polymer.
Fujisaki H; Shiga M; Moritsugu K; Kidera A
J Chem Phys; 2013 Aug; 139(5):054117. PubMed ID: 23927253
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]