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HHPred specifications

Information


Unique identifier OMICS_16760
Name HHPred
Interface Web user interface
Restrictions to use None
Input data The protein sequence or MSA.
Output data The predicted structure.
Output format .PDB
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/HHpred_/_HHsearch

Maintainer


  • person_outline Johannes Soding

Information


Unique identifier OMICS_16760
Name HHPred
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A file containing user’s query sequence (in fasta format) or a *.a3m file (as generated by e.g. hhblits).
Input format .FASTA
Output data The predicted structure.
Output format .PDB
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
HH-suite library, hhpred databases, MODELLER
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/HHpred_/_HHsearch

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Maintainer


  • person_outline Johannes Soding

Publication for HHPred

HHPred citations

 (977)
library_books

Microscopic and Molecular Evidence of the First Elasmobranch Adomavirus, the Cause of Skin Disease in a Giant Guitarfish, Rhynchobatus djiddensis

2018
MBio
PMCID: 5954223
PMID: 29764943
DOI: 10.1128/mBio.00185-18

[…] LO4 to LO8 ORFs that share 26 to 35% protein identities () and do not resemble any papillomavirus or polyomavirus proteins by sequence homology or length. However, a structural homology search using HHpred showed that they share weak homology (score, 53; identities, 18%) to adenoviruses, which also encode a tandem array of multiple capsid subunits.Molecular findings suggest that only infection by […]

library_books

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine based chemotherapy

2018
BMC Cancer
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] needed, so a template or crystal structure that contains the SNP’s region is retrieved by using either “NCBI-BLAST” of the protein sequence against PDB (E-Value cutoff 0.001 with BLOSUM62 matrix) or HHPRED against PDB (E-Value cutoff 0.001) on ANNOTATOR []. If there is a crystal structure available where the SNP is located, we use the crystal structure as an input to FoldX. For SNPs in proteins w […]

library_books

Complete Genome Sequences of Bacillus Phages Janet and OTooleKemple52

2018
Genome Announc
PMCID: 5946042
PMID: 29748396
DOI: 10.1128/genomeA.00083-18

[…] u/computer.htm), which includes the open reading frame (ORF) prediction tools GeneMark () and Glimmer () and the tRNA prediction tool ARAGORN (). Functional analysis was performed using BLASTp () and HHpred ().Janet has a length of 160,705 bp, with terminal repeats of 2,434 bp, while OTooleKemple52 (OTK52) has a genome length of 161,807 bp, with terminal repeats of 2,426 bp. The genomes have 38% G […]

library_books

Systematic mapping of contact sites reveals tethers and a function for the peroxisome mitochondria contact

2018
Nat Commun
PMCID: 5932058
PMID: 29720625
DOI: 10.1038/s41467-018-03957-8

[…] Pex34 is a 144 amino-acid peroxisomal membrane protein that affects peroxisome growth and division by an unknown mechanism. Since Pex34 shares a remote homology with Pex11 (using HHpred), that was previously suggested to serve as a PerMit tether, we examined if Pex34 also has the capacity to directly tether the PerMit contact.To this end, we found that Pex34 overexpression lea […]

library_books

Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites

2018
Nat Commun
PMCID: 5923384
PMID: 29703975
DOI: 10.1038/s41467-018-03923-4

[…] sporidia (AncNTTMic) and Microsporidia and Rozella (AncNTTRoz/Mic) (Fig. ). Both inferred ancestral sequences contain residues known to be functionally important for NTTs (Supplementary Fig.  & ) and HHPRED analyses demonstrate that, like contemporary NTTs, they are members of the Major Facilitator Superfamily (MFS; Supplementary Table ). Analyses of the inferred secondary structure of the two anc […]

call_split

Sak4 of Phage HK620 Is a RecA Remote Homolog With Single Strand Annealing Activity Stimulated by Its Cognate SSB Protein

2018
Front Microbiol
PMCID: 5928155
PMID: 29740405
DOI: 10.3389/fmicb.2018.00743
call_split See protocol

[…] as SSB produced by phages Lc-Nu and PhiAT3 were homologous to experimentally proven SSB, these two proteins were compared to the PDB70 database available at http://toolkit.lmb.uni-muenchen.de/ using HHpred. Each of them identified as best hit the SSB of E. coli (probability above 99%, with 14 and 17% sequence identity). However, SSBHK620 did not match directly with SSB of E. coli with HHpred. […]

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HHPred institution(s)
Gene Center and Center for Integrated Protein Science (Munich), Ludwig-Maximilians-University Munich, Munich, Germany

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