349 related articles for article (PubMed ID: 25153688)
1. Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics.
Doshi U; Hamelberg D
Biochim Biophys Acta; 2015 May; 1850(5):878-888. PubMed ID: 25153688
[TBL] [Abstract][Full Text] [Related]
2. Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.
Doshi U; Hamelberg D
J Phys Chem Lett; 2014 Apr; 5(7):1217-24. PubMed ID: 26274474
[TBL] [Abstract][Full Text] [Related]
3. Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions.
Doshi U; Hamelberg D
J Chem Theory Comput; 2012 Nov; 8(11):4004-12. PubMed ID: 26605567
[TBL] [Abstract][Full Text] [Related]
4. Enhanced molecular dynamics sampling of drug target conformations.
Rodriguez-Bussey IG; Doshi U; Hamelberg D
Biopolymers; 2016 Jan; 105(1):35-42. PubMed ID: 26352326
[TBL] [Abstract][Full Text] [Related]
5. Accelerated molecular dynamics simulations of protein folding.
Miao Y; Feixas F; Eun C; McCammon JA
J Comput Chem; 2015 Jul; 36(20):1536-49. PubMed ID: 26096263
[TBL] [Abstract][Full Text] [Related]
6. Gaussian Accelerated Molecular Dynamics in NAMD.
Pang YT; Miao Y; Wang Y; McCammon JA
J Chem Theory Comput; 2017 Jan; 13(1):9-19. PubMed ID: 28034310
[TBL] [Abstract][Full Text] [Related]
7. Thermodynamics of Protein Folding Studied by Umbrella Sampling along a Reaction Coordinate of Native Contacts.
Meshkin H; Zhu F
J Chem Theory Comput; 2017 May; 13(5):2086-2097. PubMed ID: 28355066
[TBL] [Abstract][Full Text] [Related]
8. Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations.
Peng X; Zhang Y; Li Y; Liu Q; Chu H; Zhang D; Li G
J Chem Theory Comput; 2018 Mar; 14(3):1216-1227. PubMed ID: 29394067
[TBL] [Abstract][Full Text] [Related]
9. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.
van der Vaart A
Biochim Biophys Acta; 2015 May; 1850(5):1091-1098. PubMed ID: 25161164
[TBL] [Abstract][Full Text] [Related]
10. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.
Buchner GS; Murphy RD; Buchete NV; Kubelka J
Biochim Biophys Acta; 2011 Aug; 1814(8):1001-20. PubMed ID: 20883829
[TBL] [Abstract][Full Text] [Related]
11. Enhanced sampling techniques in molecular dynamics simulations of biological systems.
Bernardi RC; Melo MCR; Schulten K
Biochim Biophys Acta; 2015 May; 1850(5):872-877. PubMed ID: 25450171
[TBL] [Abstract][Full Text] [Related]
12. Targeting electrostatic interactions in accelerated molecular dynamics with application to protein partial unfolding.
Flores-Canales JC; Kurnikova M
J Chem Theory Comput; 2015 Jun; 11(6):2550-9. PubMed ID: 26575554
[TBL] [Abstract][Full Text] [Related]
13. Studying functional dynamics in bio-molecules using accelerated molecular dynamics.
Markwick PR; McCammon JA
Phys Chem Chem Phys; 2011 Dec; 13(45):20053-65. PubMed ID: 22015376
[TBL] [Abstract][Full Text] [Related]
14. Accelerated molecular dynamics in computational drug design.
Wereszczynski J; McCammon JA
Methods Mol Biol; 2012; 819():515-24. PubMed ID: 22183555
[TBL] [Abstract][Full Text] [Related]
15. Modelling proteins: conformational sampling and reconstruction of folding kinetics.
Klenin K; Strodel B; Wales DJ; Wenzel W
Biochim Biophys Acta; 2011 Aug; 1814(8):977-1000. PubMed ID: 20851219
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. General trends of dihedral conformational transitions in a globular protein.
Miao Y; Baudry J; Smith JC; McCammon JA
Proteins; 2016 Apr; 84(4):501-14. PubMed ID: 26799251
[TBL] [Abstract][Full Text] [Related]
18. Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules.
Oshima H; Re S; Sugita Y
J Chem Theory Comput; 2019 Oct; 15(10):5199-5208. PubMed ID: 31539245
[TBL] [Abstract][Full Text] [Related]
19. Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics.
Miao Y
J Chem Phys; 2018 Aug; 149(7):072308. PubMed ID: 30134710
[TBL] [Abstract][Full Text] [Related]
20. Comparing the intrinsic dynamics of multiple protein structures using elastic network models.
Fuglebakk E; Tiwari SP; Reuter N
Biochim Biophys Acta; 2015 May; 1850(5):911-922. PubMed ID: 25267310
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
