Gibbs sampling and helix-cap motifs

Gibbs sampling and helix-cap motifs

Protein backbones have characteristic secondary structures, including alpha-helices and beta-sheets. Which structure is adopted locally is strongly biased by the local amino acid sequence of the protein. Accurate (probabilistic) mappings from sequence to structure are valuable for both secondary-structure prediction and protein design. For the case of alpha-helix caps, we test whether the infor...

Regulatory Motifs, Gibbs Sampling, and EM

A Gibbs sampling approach to detection of tree motifs.

This paper introduces a method to detect tree patterns (tree motifs) in a database of rooted unordered labeled trees. The method can be viewed as an extension of the Gibbs sampling approach to detect sequence motifs. Basically, we enumerate tree topologies and for each topology we seek within the database for tree motifs with the given topology. A tree motif can be detected by matching the tree...

Helix-turn-helix motifs in unsolvated peptides.

The conformations of unsolvated Ac-A14KG3A14K + 2H+ (Ac = acetyl, A = alanine, K = lysine, G = glycine) have been examined by ion mobility measurements and molecular dynamics simulations. This peptide was designed as a model helix-turn-helix motif. It was found to adopt three distinct geometries which were assigned to an extended helical conformation which is only stable at low temperatures (<2...

On particle Gibbs sampling

The particle Gibbs sampler is a Markov chain Monte Carlo (MCMC) algorithm to sample from the full posterior distribution of a state-space model. It does so by executing Gibbs sampling steps on an extended target distribution defined on the space of the auxiliary variables generated by an interacting particle system. This paper makes the following contributions to the theoretical study of this a...