Quality measures for protein alignment benchmarks

Domain assignment for protein structures using a consensus approach: Characterization and analysis

(2010) Susan Jones et al.   PROTEIN SCIENCE

Optimizing substitution matrix choice and gap parameters for sequence alignment

(2009) Robert C Edgar   BMC BIOINFORMATICS

Advances and pitfalls of protein structural alignment

(2009) Hitomi Hasegawa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

(2008) Amarendran R Subramanian et al.   Algorithms for Molecular Biology

The SOCS Box Domain of SOCS3: Structure and Interaction with the ElonginBC-Cullin5 Ubiquitin Ligase

(2008) Jeffrey J. Babon et al.   JOURNAL OF MOLECULAR BIOLOGY