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Gabriel Studer's avatar
Studer Gabriel authored
Minimum length for a chain in the target structure
to be considered in chain mapping. The chain mapping algorithm first
performs an all vs. all pairwise sequence alignment to identify
"equal" chains within the target structure. We go for simple sequence
identity there. Short sequences can be problematic as they may
produce high sequence identity alignments by pure chance.

BUT: if you're scoring peptides or short nucleotides, you
really want to be able to reduce the default thresholds
(pep: 10, nuc: 4)
341783cc
History
================= OpenStructure molecular modelling 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 you 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

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 

================= The OpenStructure Team =======================================