HH-suite3 for fast remote homology detection and deep protein annotation

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

New CRISPR–Cas systems from uncultivated microbes

(2016) David Burstein et al.   NATURE

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains

(2016) David R. Fidler et al.   TRAFFIC

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

(2014) Marco Biasini et al.   NUCLEIC ACIDS RESEARCH

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discriminative modelling of context-specific amino acid substitution probabilities

(2012) Christof Angermüller et al.   BIOINFORMATICS

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

(2011) Torbjørn Rognes   BMC BIOINFORMATICS

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

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

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

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

(2011) Michael Remmert et al.   NATURE METHODS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison

(2010) Mindaugas Margelevičius et al.   BMC BIOINFORMATICS

Comparison of sequence profiles. Strategies for structural predictions using sequence information

(2010) Leszek Rychlewski et al.   PROTEIN SCIENCE

De novo identification of highly diverged protein repeats by probabilistic consistency

(2008) A. Biegert et al.   BIOINFORMATICS

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

(2008) Svetlin A Manavski et al.   BMC BIOINFORMATICS

SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model

(2008) Wei Zhang et al.   PLoS One