|
|
|
|
| LEADER |
01000naa a22002652 4500 |
| 001 |
NLM329461613 |
| 003 |
DE-627 |
| 005 |
20231225205154.0 |
| 007 |
cr uuu---uuuuu |
| 008 |
231225s2021 xx |||||o 00| ||eng c |
| 024 |
7 |
|
|a 10.1002/jcc.26736
|2 doi
|
| 028 |
5 |
2 |
|a pubmed24n1098.xml
|
| 035 |
|
|
|a (DE-627)NLM329461613
|
| 035 |
|
|
|a (NLM)34402552
|
| 040 |
|
|
|a DE-627
|b ger
|c DE-627
|e rakwb
|
| 041 |
|
|
|a eng
|
| 100 |
1 |
|
|a Kogut, Mateusz
|e verfasserin
|4 aut
|
| 245 |
1 |
0 |
|a Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures
|
| 264 |
|
1 |
|c 2021
|
| 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 31.01.2022
|
| 500 |
|
|
|a Date Revised 31.01.2022
|
| 500 |
|
|
|a published: Print-Electronic
|
| 500 |
|
|
|a Citation Status MEDLINE
|
| 520 |
|
|
|a © 2021 Wiley Periodicals LLC.
|
| 520 |
|
|
|a Pseudopotentials for the chemical cross-links comprising the glutamic- and aspartic-acid side chains bridged with adipic- (ADH) or pimelic-acid hydrazide (PDH), and the lysine side chains bridged with glutaric (BS2 G) or suberic acid (BS3 ) for coarse-grained cross-link-assisted simulations were determined by canonical molecular dynamics with the Amber14sb force field. The potentials depend on the distance between side-chain ends and on side-chain orientation, this preventing from making cross-link contacts across the globule in simulations. The potentials were implemented in the UNRES coarse-grained force field and their effect on the quality of models was assessed with 11 monomeric and 1 dimeric proteins, using synthetic or experimental cross-link data. Simulations with the new potentials resulted in improvement of the generated models compared to unrestrained simulations in more instances compared to those with the statistical potentials
|
| 650 |
|
4 |
|a Journal Article
|
| 650 |
|
4 |
|a Research Support, Non-U.S. Gov't
|
| 650 |
|
4 |
|a chemical cross-link mass spectroscopy
|
| 650 |
|
4 |
|a coarse-grained modeling
|
| 650 |
|
4 |
|a molecular dynamics
|
| 650 |
|
4 |
|a potentials of mean force
|
| 650 |
|
7 |
|a Proteins
|2 NLM
|
| 700 |
1 |
|
|a Gong, Zhou
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Tang, Chun
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Liwo, Adam
|e verfasserin
|4 aut
|
| 773 |
0 |
8 |
|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 42(2021), 29 vom: 05. Nov., Seite 2054-2067
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
|
| 773 |
1 |
8 |
|g volume:42
|g year:2021
|g number:29
|g day:05
|g month:11
|g pages:2054-2067
|
| 856 |
4 |
0 |
|u http://dx.doi.org/10.1002/jcc.26736
|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 42
|j 2021
|e 29
|b 05
|c 11
|h 2054-2067
|