COMPASS server for homology detection: improved statistical accuracy, speed and functionality

By Ruslan I. Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin. 2009

27 citations recorded by the source corpus.

COMPASS is a profile-based method for the detection of remote sequence similarity and the prediction of protein structure. Here we describe a recently improved public web server of COMPASS, http://prodata.swmed.edu/compass. The server features three major developments: (i) improved statistical accuracy; (ii) increased speed from parallel implementation; and (iii) new functional features facilitating structure prediction. These features include visualization tools that allow the user to quickly and effectively analyze specific local structural region predictions suggested by COMPASS alignments. As an application example, we describe the structural, evolutionary and functional analysis of a protein with unknown function that served as a target in the recent CASP8 (Critical Assessment of Techniques for Protein Structure Prediction round 8). URL: http://prodata.swmed.edu/compass

Subfields: Ecology, Molecular Biology, Spectroscopy

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In Molecular Biology

1. Bin Liu
2. Junjie Chen
3. Xiaolong Wang
4. Mingyue Guo

In Spectroscopy

1. Xiaolong Wang
2. Junjie Chen
3. Mingyue Guo
4. Bin Liu

Citations in the corpus

• A comprehensive review and comparison of different computational methods for protein remote homology detection (2018, background): “Methods in the third category are based on profile–profile alignment, which search a profile query against a database of profiles, such as COMPASS [34, 35], FFAS [36] and COMA [37].”