English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Optimal superpositioning of flexible molecule ensemble.

Gapsys, V., & de Groot, B. L. (2013). Optimal superpositioning of flexible molecule ensemble. Biophysical Journal, 104(1), 196-207. doi:10.1016/j.bpj.2012.11.003.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-CAD3-D Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0029-793C-A
Genre: Journal Article

Files

show Files
hide Files
:
1690423.pdf (Publisher version), 2MB
Name:
1690423.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-
:
1690423_Suppl.pdf (Supplementary material), 10MB
Name:
1690423_Suppl.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-

Creators

show
hide
 Creators:
Gapsys, V.1, Author              
de Groot, B. L.1, Author              
Affiliations:
1Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578573              

Content

show
hide
Free keywords: -
 Abstract: Analysis of the internal dynamics of a biological molecule requires the successful removal of overall translation and rotation. Particularly for flexible or intrinsically disordered peptides, this is a challenging task due to the absence of a well-defined reference structure that could be used for superpositioning. In this work, we started the analysis with a widely known formulation of an objective for the problem of superimposing a set of multiple molecules as variance minimization over an ensemble. A negative effect of this superpositioning method is the introduction of ambiguous rotations, where different rotation matrices may be applied to structurally similar molecules. We developed two algorithms to resolve the suboptimal rotations. The first approach minimizes the variance together with the distance of a structure to a preceding molecule in the ensemble. The second algorithm seeks for minimal variance together with the distance to the nearest neighbors of each structure. The newly developed methods were applied to molecular-dynamics trajectories and normal-mode ensembles of the Aβ peptide, RS peptide, and lysozyme. These new (to our knowledge) superpositioning methods combine the benefits of variance and distance between nearest-neighbor(s) minimization, providing a solution for the analysis of intrinsic motions of flexible molecules and resolving ambiguous rotations.

Details

show
hide
Language(s): eng - English
 Dates: 2013-01-08
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1016/j.bpj.2012.11.003
 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: 104 (1) Sequence Number: - Start / End Page: 196 - 207 Identifier: -