English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
 
 
DownloadE-Mail
  GROmaρs: A GROMACS-based toolset to analyze density maps derived from molecular dynamics simulations.

Briones, R., Blau, C., Kutzner, C., de Groot, B. L., & Aponte-Santamaría, C. (2019). GROmaρs: A GROMACS-based toolset to analyze density maps derived from molecular dynamics simulations. Biophysical Journal, 116(1), 4-11. doi:10.1016/j.bpj.2018.11.3126.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/21.11116/0000-0002-B3C5-5 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-3968-9
Genre: Journal Article

Files

show Files
hide Files
:
3016284.pdf (Preprint), 2MB
 
File Permalink:
-
Name:
3016284.pdf
Description:
-
Visibility:
Private (embargoed till 2020-01-31)
MIME-Type / Checksum:
application/pdf
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-

Locators

show

Creators

show
hide
 Creators:
Briones, R.1, Author              
Blau, C.2, Author              
Kutzner, C.2, Author              
de Groot, B. L.1, Author              
Aponte-Santamaría, C., Author
Affiliations:
1Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578573              
2Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

Content

show
hide
Free keywords: -
 Abstract: We introduce a computational toolset, named GROmaρs, to obtain and compare time-averaged density maps from molecular dynamics simulations. GROmaρs efficiently computes density maps by fast multi-Gaussian spreading of atomic densities onto a three-dimensional grid. It complements existing map-based tools by enabling spatial inspection of atomic average localization during the simulations. Most importantly, it allows the comparison between computed and reference maps (e.g., experimental) through calculation of difference maps and local and time-resolved global correlation. These comparison operations proved useful to quantitatively contrast perturbed and control simulation data sets and to examine how much biomolecular systems resemble both synthetic and experimental density maps. This was especially advantageous for multimolecule systems in which standard comparisons like RMSDs are difficult to compute. In addition, GROmaρs incorporates absolute and relative spatial free-energy estimates to provide an energetic picture of atomistic localization. This is an open-source GROMACS-based toolset, thus allowing for static or dynamic selection of atoms or even coarse-grained beads for the density calculation. Furthermore, masking of regions was implemented to speed up calculations and to facilitate the comparison with experimental maps. Beyond map comparison, GROmaρs provides a straightforward method to detect solvent cavities and average charge distribution in biomolecular systems. We employed all these functionalities to inspect the localization of lipid and water molecules in aquaporin systems, the binding of cholesterol to the G protein coupled chemokine receptor type 4, and the identification of permeation pathways through the dermicidin antimicrobial channel. Based on these examples, we anticipate a high applicability of GROmaρs for the analysis of molecular dynamics simulations and their comparison with experimentally determined densities.

Details

show
hide
Language(s): eng - English
 Dates: 2018-12-012019-01-08
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1016/j.bpj.2018.11.3126
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Biophysical Journal
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 116 (1) Sequence Number: - Start / End Page: 4 - 11 Identifier: -