OpenStructure statistics

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Citations per year

Number of citations per year for the bioinformatics software tool OpenStructure
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Tool usage distribution map

This map represents all the scientific publications referring to OpenStructure per scientific context
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OpenStructure specifications

Information


Unique identifier OMICS_09826
Name OpenStructure
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.4.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Torsten Schwede

Publications for OpenStructure

OpenStructure citations

 (8)
library_books

Modeling protein quaternary structure of homo and hetero oligomers beyond binary interactions by homology

2017
Sci Rep
PMCID: 5585393
PMID: 28874689
DOI: 10.1038/s41598-017-09654-8

[…] ataset consists of homology models based on the alignment of the target sequence to template structures generated with PROMOD3 (Studer et al., in preparation), a comparative modelling engine based on OpenStructure. The loop candidates are selected with a database approach and are then adapted to the environment using CCD and a final candidate gets selected using statistical potentials of mean forc […]

library_books

Unidirectional Transport Mechanism in an ATP Dependent Exporter

2017
PMCID: 5364450
PMID: 28386603
DOI: 10.1021/acscentsci.7b00068

[…] OpenStructure was used for most of the analyses of the conformational changes along the simulation trajectories. The NBS “binding distance” was defined as the distance between the signature motif (res […]

library_books

A computational protocol to evaluate the effects of protein mutants in the kinase gatekeeper position on the binding of ATP substrate analogues

2017
BMC Res Notes
PMCID: 5319021
PMID: 28219448
DOI: 10.1186/s13104-017-2428-9

[…] ied by this approach, the analogue was considered to act as substrate for the native target and thus not further considered. The method was implemented in Python 2.5.4 and contains functions from the OpenStructure software framework [].In the second step, the interaction between potential protein mutants and ligand analogues was evaluated using a protein–ligand scoring function. Amino acids at pos […]

library_books

Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations

2016
BMC Bioinformatics
PMCID: 4830014
PMID: 27071656
DOI: 10.1186/s12859-016-1003-z

[…] SetBoolProp method, setting them to True for lipids in chain M (lines 13-15, Scheme ) and False for all the other lipids (lines 17-19, Scheme ). Such custom properties are called GenericProperties in OpenStructure and can be attached to atoms, residues or chains.Scheme 4Scheme 5Scheme 6We are now ready to calculate the lipid tilts and splays by calling the AnalyzeLipidTiltAndSplay function (lines […]

library_books

Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane)

2014
Bioinformatics
PMCID: 4147910
PMID: 25161240
DOI: 10.1093/bioinformatics/btu457

[…] ng computationally expensive tasks in a C++ layer. All functionality is made fully accessible from the Python language and can directly be embedded into the computational structural biology framework OpenStructure (, ), allowing to assemble custom assessment pipelines to address more specific requirements. […]

library_books

Protein and Lipid Interactions Driving Molecular Mechanisms of in meso Crystallization

2014
J Am Chem Soc
PMCID: 3985912
PMID: 24494670
DOI: 10.1021/ja4129839

[…] magnitude higher than points on the surface). The error bars in the figures discussed in the show the width of the distributions measured as p75 – p25.All analyses and visualizations were done using OpenStructure., […]


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OpenStructure institution(s)
Biozentrum, Universität Basel, Basel, Switzerland

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