Increasing the precision of comparative models with YASARA NOVA—a self‐parameterizing force field

By Elmar Krieger, G. Koraimann, G. Vriend. 2002

1,507 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

A series of PDB related databases for everyday needs (2010, methodology): “For this purpose we developed a Python plug-in for the free molecular modelling program ‘YASARA View’ (42), available from www.yasara.org/ viewdl/.”
Making optimal use of empirical energy functions: Force‐field parameterization in crystal space (2004, methodology): “15 While it takes nanosecond simulations to check if a homology model improves during a molecular dynamics run, only picosec-onds are required to minimize a real experimental structure.”
Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments (2008, methodology): “All protein graphics in this article were generated with the YASARA software package [52] and PyMOL [53].”
The PDB_REDO server for macromolecular structure model optimization (2014, background): “License requirements for YASARA and FoldX have been waived by their respective developers because only small parts of the programs’ functionality are used.”
Mutations in SMAD3 cause a syndromic form of aortic aneurysms and dissections with early-onset osteoarthritis (2011, methodology): “The effects of the mutations on the protein structure and function were predicted using molecular graphics, modeling and simulation programs from YASARA NOV”
PDB_REDO: constructive validation, more than just looking for errors (2012, background): “We currently use molecular scenes from YASARA to highlight changes in the model, but this requires that installation of software and can only show one thing at a time.”