HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure

(2011) Zafer Aydin et al.   BMC BIOINFORMATICS

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

(2011) Johannes Söding et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Homologous over-extension: a challenge for iterative similarity searches

(2010) Mileidy W. Gonzalez et al.   NUCLEIC ACIDS RESEARCH

PDBselect 1992–2009 and PDBfilter-select

(2009) Sven Griep et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Sequence context-specific profiles for homology searching

(2009) A. Biegert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo identification of highly diverged protein repeats by probabilistic consistency

(2008) A. Biegert et al.   BIOINFORMATICS