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Citations per year

Number of citations per year for the bioinformatics software tool HHsuite

Tool usage distribution map

This map represents all the scientific publications referring to HHsuite per scientific context
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HHsuite specifications


Unique identifier OMICS_28407
Name HHsuite
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.0-beta.3
Stability Stable
C/C++ compiler, CMake, pdbx python library
Maintained Yes


  • HHblits




No version available



  • person_outline Johannes Soeding

Publications for HHsuite

HHsuite citations


Discovery of Culex pipiens associated tunisia virus: a new ssRNA(+) virus representing a new insect associated virus family

Virus Evol
PMCID: 5763275
PMID: 29340209
DOI: 10.1093/ve/vex040

[…] Protein homology searches were performed on all translated ORFs of the 22 transcriptomes using the accurate and sensitive HHblits program implemented in the HHSuite package (; ). The Nr20 NCBI protein database, a clustered version of the protein nonredundant database from NCBI down to a maximum pairwise sequence identity of 20% protein, was used as a sear […]


Comparative Analysis of 37 Acinetobacter Bacteriophages

PMCID: 5795418
PMID: 29295549
DOI: 10.3390/v10010005

[…] head of 73 × 59 nm and a 252 nm long tail that is characterised by the presence of multiple transverse disks that gives the tail a segmented appearance []. Analysis of R3177 and Bphi-B1251 ORFs using HHsuite allowed for the prediction of additional structural, replication and maintenance proteins. Examining dot plot alignment of Bphi-B1215 and R3177 shows that a number of genomic modules exhibit l […]


Iodide Binding in Sodium Coupled Cotransporters

J Chem Inf Model
PMCID: 5744185
PMID: 29131623
DOI: 10.1021/acs.jcim.7b00521

[…] dels of both proteins, using the identical modeling protocol. We searched for a template structure using Psi-Blast v2.2.30 on the nonredundant Protein Data Bank (PDB) database, as well as HHPred from HHsuite v3.0 on a nonredundant PDB sequence database clustered at 70% sequence identity. The structure of the sodium/galactose transporter from Vibrio parahemolyticus (vSGLT), in an inward-facing conf […]


Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non enveloped Fish Viruses

PMCID: 5604429
PMID: 28867387
DOI: 10.1016/j.chom.2017.07.019

[…] ), we followed the strategy used for P with the addition that predicted protein secondary structure was taken into account during profile-based alignments. To this end, we used the HHalign program of HHsuite v2.0.16 () with the default parameter configuration. HHalign results were incorporated manually into the SeaView-based alignment construction. Graphical representations of sequence alignments […]


An overview of comparative modelling and resources dedicated to large scale modelling of genome sequences

Acta Crystallogr D Struct Biol
PMCID: 5571743
PMID: 28777078
DOI: 10.1107/S2059798317008920

[…] ecent CASPs, such as Robetta (Kim et al., 2004; Ovchinnikov et al., 2017), MULTICOM (Li et al., 2015) and nns (Joo et al., 2016). HHsearch scans query sequences against a library of HMMs (built using HHsuite) and outputs a list of structural matches and corresponding query–template matches. Our FunFams pipeline first assigns a query sequence to a FunFam using HMMer3 (Eddy, 2011) and then selects t […]


Large scale structure prediction by improved contact predictions and model quality assessment

PMCID: 5870574
PMID: 28881974
DOI: 10.1093/bioinformatics/btx239
call_split See protocol

[…] mily by the representative sequence. The representative sequence of a Pfam domain with known structure is set to be the protein sequence ranked first by HHsearch against the PDB database bundled with HHsuite () (date: September 7, 2016)The test dataset was generated from 626 Pfam domains that were randomly selected from 6925 domains with known structure that are longer than 50 residues.From the re […]

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