Background: Although both conservation and correlated mutation (CM) are important information reflecting the different sorts of context in multiple sequence alignment, most of ali...
In this paper we investigate the protein sequence design (PSD) problem (also known as the inverse protein folding problem) under the Canonical model 4 on 2D and 3D lattices [12, 25...
Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robe...
Background: Structural similarities among proteins can provide valuable insight into their functional mechanisms and relationships. As the number of available three-dimensional (3...
Background: Recent approaches for predicting the three-dimensional (3D) structure of proteins such as de novo or fold recognition methods mostly rely on simplified energy potentia...
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...