THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

By Douglas L. Theobald, Deborah S. Wuttke. 2006

211 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Large-scale determination of previously unsolved protein structures using evolutionary information (2015, neutral): “1 ( Theobald and Wuttke, 2006 ).”
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions (2011, unknown): “Using the maximum-likelihood superposition software program, Theseus (Theobald and Wuttke, 2006), each of the 100 resulting decoys was translated and rotated closest to the idealized structure.”
The Expanded FindCore Method for Identification of a Core Atom Set for Assessment of Protein Structure Prediction (2014, background): “27,28 However, in the absence of a well-defined sampling distribution, such methods may not produce maximum likelihood superimpositions.”
Accurate Structural Correlations from Maximum Likelihood Superpositions (2008, methodology): “For input, THESEUS takes a set of standard PDB formatted structure coordinate files (http://www. wwpdb.org/docs.html [39,40]).”
AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. (2012, methodology): “The largest of these subclusters, which must contain more than one decoy to proceed, was structurally aligned using THESEUS and proceeded to side-chain treatment.”
Analysis of CASP8 targets, predictions and assessment methods (2009, methodology): “First, for each structure all NMR models (20 or 10) were superimposed with Theseus, a program by Theobald and Wuttke (7) that uses a maximum likelihood method for multiple structure alignment.”
CATH: comprehensive structural and functional annotations for genome sequences (2014, methodology): “The algorithm achieves this effect by exploiting the SSAP residuepair scores for each position in the alignment to identify structurally divergent positions and then disregarding these positions when superposing the structures (14).”