Graph Theory-Based Sequence Descriptors as Remote Homology Predictors

Topos based homology theory

In this paper we extend the Eilenberg-Steenrod axiomatic description of a homology theory from the category of topological spaces to an arbitrary category and, in particular, to a topos. Implicit in this extension is an extension of the notions of homotopy and excision. A general discussion of such homotopy and excision structures on a category is given along with several examples including the...

Improved performance of sequence search algorithms in remote homology detection

The protein sequence space is vast and diverse, spanning across different families. Biologically meaningful relationships exist between proteins at superfamily level. However, it is highly challenging to establish convincing relationships at the superfamily level by means of simple sequence searches. It is necessary to design a rigorous sequence search strategy to establish remote homology rela...

Remote Homology Detection Using Local Sequence-Structure Correlations

Remote homology detection refers to the problem of detecting protein homology in cases of low sequence similarity. Existing methods to establish homology relationships via sequence similarity do not work well for these remote homology. In this paper, we present a new method, SVM-HMMSTR, that overcomes the reliance on sequence similarity by taking into consideration the local structure similarit...

CPHmodels-3.0—remote homology modeling using structure-guided sequence profiles

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile-profile scoring function suitable for close homology modeling. The new computational costly...

Improving Remote Homology Detection Using a Sequence Property