Background: Proteins that are similar in sequence or structure may perform different functions in nature. In such cases, function cannot be inferred from sequence or structural si...
The 3D conformation of a protein may be compactly represented in a symmetrical, square, boolean matrix of pairwise, inter-residue contacts, or "contact map". The contact...
Jingjing Hu, Xiaolan Shen, Yu Shao, Chris Bystroff...
Background: The functional annotation of proteins relies on published information concerning their close and remote homologues in sequence databases. Evidence for remote sequence ...
Charles Richard Bradshaw, Vineeth Surendranath, Bi...
Background: This paper deals with the preprocessing of protein sequences for supervised classification. Motif extraction is one way to address that task. It has been largely used ...
Background: Profile HMMs (hidden Markov models) provide effective methods for modeling the conserved regions of protein families. A limitation of the resulting domain models is th...