OpenStructure protocols

View OpenStructure computational protocol

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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

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Maintainer


  • person_outline Torsten Schwede <>

Publications for OpenStructure

OpenStructure in pipeline

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

[…] 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 […]


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OpenStructure in publications

 (7)
PMCID: 5585393
PMID: 28874689
DOI: 10.1038/s41598-017-09654-8

[…] 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 […]

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

[…] with an oscillation period of 50 fs and an oscillation decay time of 25 fs. all bonds involving hydrogen atoms are constrained using the shake algorithm. the time step for all simulations was 2 fs., 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 […]

PMCID: 5319021
PMID: 28219448
DOI: 10.1186/s13104-017-2428-9

[…] 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 […]

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

[…] the distributions of microscopic tilts and splays of the lipid components. we present here an open source implementation of the method as a set of python modules using the computational framework openstructure. these modules offer diverse algorithms typically used in the calculatation the elastic moduli, including routines to align md trajectories of complex lipidic systems, to determine […]

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

[…] 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., to evaluate the performance of our membrane finding algorithm, a comparison […]


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

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