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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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