|
|
|
|
| LEADER |
01000naa a22002652 4500 |
| 001 |
NLM251945812 |
| 003 |
DE-627 |
| 005 |
20231224163101.0 |
| 007 |
cr uuu---uuuuu |
| 008 |
231224s2015 xx |||||o 00| ||eng c |
| 024 |
7 |
|
|a 10.1002/jcc.24053
|2 doi
|
| 028 |
5 |
2 |
|a pubmed24n0839.xml
|
| 035 |
|
|
|a (DE-627)NLM251945812
|
| 035 |
|
|
|a (NLM)26284944
|
| 040 |
|
|
|a DE-627
|b ger
|c DE-627
|e rakwb
|
| 041 |
|
|
|a eng
|
| 100 |
1 |
|
|a Sakalli, Ilkay
|e verfasserin
|4 aut
|
| 245 |
1 |
0 |
|a pK(A) in proteins solving the Poisson-Boltzmann equation with finite elements
|
| 264 |
|
1 |
|c 2015
|
| 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 30.06.2016
|
| 500 |
|
|
|a Date Revised 30.09.2015
|
| 500 |
|
|
|a published: Print-Electronic
|
| 500 |
|
|
|a Citation Status MEDLINE
|
| 520 |
|
|
|a © 2015 Wiley Periodicals, Inc.
|
| 520 |
|
|
|a Knowledge on pK(A) values is an eminent factor to understand the function of proteins in living systems. We present a novel approach demonstrating that the finite element (FE) method of solving the linearized Poisson-Boltzmann equation (lPBE) can successfully be used to compute pK(A) values in proteins with high accuracy as a possible replacement to finite difference (FD) method. For this purpose, we implemented the software molecular Finite Element Solver (mFES) in the framework of the Karlsberg+ program to compute pK(A) values. This work focuses on a comparison between pK(A) computations obtained with the well-established FD method and with the new developed FE method mFES, solving the lPBE using protein crystal structures without conformational changes. Accurate and coarse model systems are set up with mFES using a similar number of unknowns compared with the FD method. Our FE method delivers results for computations of pK(A) values and interaction energies of titratable groups, which are comparable in accuracy. We introduce different thermodynamic cycles to evaluate pK(A) values and we show for the FE method how different parameters influence the accuracy of computed pK(A) values
|
| 650 |
|
4 |
|a Journal Article
|
| 650 |
|
4 |
|a Research Support, Non-U.S. Gov't
|
| 650 |
|
4 |
|a electrostatics
|
| 650 |
|
4 |
|a finite difference method
|
| 650 |
|
4 |
|a finite element method
|
| 650 |
|
4 |
|a linearized Poisson-Boltzmann equation
|
| 650 |
|
4 |
|a molecular surface
|
| 650 |
|
4 |
|a pKA value
|
| 650 |
|
4 |
|a thermodynamic cycle
|
| 650 |
|
7 |
|a Ions
|2 NLM
|
| 650 |
|
7 |
|a Proteins
|2 NLM
|
| 650 |
|
7 |
|a Muramidase
|2 NLM
|
| 650 |
|
7 |
|a EC 3.2.1.17
|2 NLM
|
| 700 |
1 |
|
|a Knapp, Ernst-Walter
|e verfasserin
|4 aut
|
| 773 |
0 |
8 |
|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 36(2015), 29 vom: 05. Nov., Seite 2147-57
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
|
| 773 |
1 |
8 |
|g volume:36
|g year:2015
|g number:29
|g day:05
|g month:11
|g pages:2147-57
|
| 856 |
4 |
0 |
|u http://dx.doi.org/10.1002/jcc.24053
|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 36
|j 2015
|e 29
|b 05
|c 11
|h 2147-57
|