PSI-BLAST is an iterative program to search a database for proteins with distant similarity to
a query sequence. We investigated over a dozen modifications to the methods used in PSI …

Homology modeling plays a central role in determining protein structure in the structural
genomics project. The importance of homology modeling has been steadily increasing …

Background HH-suite is a widely used open source software suite for sensitive sequence
similarity searches and protein fold recognition. It is based on pairwise alignment of profile …

Background BLAST is a commonly-used software package for comparing a query sequence
to a database of known sequences; in this study, we focus on protein sequences. Position …

Abstract The Robetta server (http://robetta. bakerlab. org) provides automated tools for
protein structure prediction and analysis. For structure prediction, sequences submitted to …

Motivation: Protein homology detection and sequence alignment are at the basis of protein
structure prediction, function prediction and evolution. Results: We have generalized the …

The rapid advances of high-throughput sequencing technologies dramatically prompted
metagenomic studies of microbial communities that exist at various environments …

The ability to separate correct models of protein structures from less correct models is of the
greatest importance for protein structure prediction methods. Several studies have examined …

FUGUE, a program for recognizing distant homologues by sequence-structure comparison
(http://www-cryst. bioc. cam. ac. uk/fugue/), has three key features.(1) Improved environment …

Metagenomics projects based on shotgun sequencing of populations of micro-organisms
yield insight into protein families. We used sequence similarity clustering to explore proteins …