We describe and demonstrate the effectiveness of a method of predicting protein secondary structures, sheet regions in particular, using a class of stochastic tree grammars as rep...
The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB. Each database hold...
Robbie P. Joosten, Tim A. H. te Beek, Elmar Kriege...
Abstract. A probabilistic graphical model is developed in order to detect the dependent evolution between different sites in biological sequences. Given a multiple sequence alignme...
In contrast to proteins, many classes of functionally related RNA molecules show a rather weak sequence conservation but instead a fairly well conserved secondary structure. Hence ...
Background: Structure-dependent substitution matrices increase the accuracy of sequence alignments when the 3D structure of one sequence is known, and are successful e.g. in fold ...