|
|
|
|
| LEADER |
01000naa a22002652 4500 |
| 001 |
NLM275140032 |
| 003 |
DE-627 |
| 005 |
20231225005016.0 |
| 007 |
cr uuu---uuuuu |
| 008 |
231225s2017 xx |||||o 00| ||eng c |
| 024 |
7 |
|
|a 10.1002/jcc.24923
|2 doi
|
| 028 |
5 |
2 |
|a pubmed24n0917.xml
|
| 035 |
|
|
|a (DE-627)NLM275140032
|
| 035 |
|
|
|a (NLM)28841239
|
| 040 |
|
|
|a DE-627
|b ger
|c DE-627
|e rakwb
|
| 041 |
|
|
|a eng
|
| 100 |
1 |
|
|a Lee, Kuo Hao
|e verfasserin
|4 aut
|
| 245 |
1 |
0 |
|a Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins
|
| 264 |
|
1 |
|c 2017
|
| 336 |
|
|
|a Text
|b txt
|2 rdacontent
|
| 337 |
|
|
|a ƒaComputermedien
|b c
|2 rdamedia
|
| 338 |
|
|
|a ƒa Online-Ressource
|b cr
|2 rdacarrier
|
| 500 |
|
|
|a Date Completed 30.05.2019
|
| 500 |
|
|
|a Date Revised 12.11.2023
|
| 500 |
|
|
|a published: Print-Electronic
|
| 500 |
|
|
|a Citation Status MEDLINE
|
| 520 |
|
|
|a © 2017 Wiley Periodicals, Inc.
|
| 520 |
|
|
|a Recasting temperature replica exchange (T-RE) as a special case of Gibbs sampling has led to a simple and efficient scheme for enhanced mixing (Chodera and Shirts, J. Chem. Phys., 2011, 135, 194110). To critically examine if T-RE with independence sampling (T-REis) improves conformational sampling, we performed T-RE and T-REis simulations of ordered and disordered proteins using coarse-grained and atomistic models. The results demonstrate that T-REis effectively increase the replica mobility in temperatures space with minimal computational overhead, especially for folded proteins. However, enhanced mixing does not translate well into improved conformational sampling. The convergences of thermodynamic properties interested are similar, with slight improvements for T-REis of ordered systems. The study re-affirms the efficiency of T-RE does not appear to be limited by temperature diffusion, but by the inherent rates of spontaneous large-scale conformational re-arrangements. Due to its simplicity and efficacy of enhanced mixing, T-REis is expected to be more effective when incorporated with various Hamiltonian-RE protocols. © 2017 Wiley Periodicals, Inc
|
| 650 |
|
4 |
|a Journal Article
|
| 650 |
|
4 |
|a Research Support, N.I.H., Extramural
|
| 650 |
|
4 |
|a Gibbs sampling
|
| 650 |
|
4 |
|a conformational ensemble
|
| 650 |
|
4 |
|a disordered proteins
|
| 650 |
|
4 |
|a enhanced sampling
|
| 650 |
|
4 |
|a independence sampling
|
| 650 |
|
4 |
|a replica exchange
|
| 650 |
|
7 |
|a Intrinsically Disordered Proteins
|2 NLM
|
| 650 |
|
7 |
|a Proteins
|2 NLM
|
| 700 |
1 |
|
|a Chen, Jianhan
|e verfasserin
|4 aut
|
| 773 |
0 |
8 |
|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 38(2017), 30 vom: 15. Nov., Seite 2632-2640
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
|
| 773 |
1 |
8 |
|g volume:38
|g year:2017
|g number:30
|g day:15
|g month:11
|g pages:2632-2640
|
| 856 |
4 |
0 |
|u http://dx.doi.org/10.1002/jcc.24923
|3 Volltext
|
| 912 |
|
|
|a GBV_USEFLAG_A
|
| 912 |
|
|
|a SYSFLAG_A
|
| 912 |
|
|
|a GBV_NLM
|
| 912 |
|
|
|a GBV_ILN_350
|
| 951 |
|
|
|a AR
|
| 952 |
|
|
|d 38
|j 2017
|e 30
|b 15
|c 11
|h 2632-2640
|