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Gabriel Studer's avatar
ligand scoring: allow dist based connectivity heuristic for ligands from mmCIF
Studer Gabriel authored 
The default behaviour is to only allow ligands from mmCIF if they're
present in the PDB chemical component dictionary. Reason for that is
the connectivity information we get from there. Actively enabling this
flag in the compare-ligand-structures action allows to use a distance
based heuristic as fallback if the ligand is not in the dicitonary.
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README.md

OpenStructure - A computational structural biology framework

OpenStructure provides a modular, flexible, molecular modelling environment which allows to integrate, process and visualize information of different origin such as sequences, alignments and 3D structures.

Please refer to www.openstructure.org for more information and documentation.

Thank you for your interest and enjoy the straightforward way of handling protein structure data!

Please do not hesitate to contact us for feedback or troubleshooting:

openstructure-users@maillist.unibas.ch

OpenStructure Installation

For a simple and portable setup, we recommend using a containerized solution. OpenStructure provides its own Docker container registry, making deployment easier. Deploying a docker image just needs a docker pull which typically finishes in about a minute depending on your local hardware and internet connection. Singularity containers bootstrap from the docker container but must be built by the user. Detailed instructions can be found here:

OpenStructure is developed and tested across various Linux distributions. You can find detailed build instructions and a list of required dependencies here: https://openstructure.org/docs/install/

Getting started

The installation and container instructions will help you set up OpenStructure for scripting. Additionally, here are some advanced use cases worth highlighting.

Benchmarking and Scoring

OpenStructure implements a benchmarking suite for comparing macromolecular complexes. To get started, check out the examples in the examples/scoring directory of this repository.

Modeling

ProMod3 is a fully featured modeling engine built on top of OpenStructure. It powers the SWISS-MODEL web server and provides advanced modeling capabilities. Learn more here:

ProMod3 Documentation

Cite Us

If you like our software and have used it in your research project, please cite the following paper on OpenStructure:

M. Biasini, T. Schmidt, S. Bienert, V. Mariani, G. Studer, J. Haas, N. Johner, A.D. Schenk, A. Philippsen and T. Schwede, OpenStructure: an integrated software framework for computational structural biology, Acta Cryst., 2013

If you use the code or binary in OpenStructure to compute lDDT scores, please also cite the following reference:

V. Mariani, M. Biasini, A. Barbato, T. Schwede, lDDT : A local superposition- free score for comparing protein structures and models using distance difference tests, Bioinformatics, 2013

If you use the code in OpenStructure to compute QS scores, please also cite the following reference:

M. Bertoni, F. Kiefer, M. Biasini, L. Bordoli, T. Schwede, Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology, Scientific Reports, 2017