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 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 …

Background Alignment of large and diverse sequence sets is a common task in biological
investigations, yet there remains considerable room for improvement in alignment quality …

We describe MUSCLE, a new computer program for creating multiple alignments of protein
sequences. Elements of the algorithm include fast distance estimation using k mer counting …

Background In a previous paper, we introduced MUSCLE, a new program for creating
multiple alignments of protein sequences, giving a brief summary of the algorithm and …

Comparative protein structure modeling predicts the three‐dimensional structure of a given
protein sequence (target) based primarily on its alignment to one or more proteins of known …

Functional characterization of a protein sequence is one of the most frequent problems in
biology. This task is usually facilitated by accurate three‐dimensional (3‐D) structure of the …

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

Publisher Summary Functional characterization of a protein sequence is one of the most
frequent problems in biology. This task is usually facilitated by accurate three-dimensional …