HOMA – Create Homology models of a protein with unknown Structure

HOMA

:: DESCRIPTION

HOMA (Homology Modeling Automatically) is a web-based interface that can create homology models of a protein with unknown structure (the target or query protein) based on a homologous protein with known structure (the template protein).

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web BRowser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteins. 2008 Jan 1;70(1):105-18.
Assessing model accuracy using the homology modeling automatically software.
Bhattacharya A, Wunderlich Z, Monleon D, Tejero R, Montelione GT.

MEDELLER – Homology-Based Coordinate Generation for Membrane Proteins

MEDELLER

:: DESCRIPTION

MEDELLER, a MP(Membrane proteins)-specific homology-based coordinate generation method,  which is optimized to build highly reliable core models.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Nov 15;26(22):2833-40. doi: 10.1093/bioinformatics/btq554. Epub 2010 Oct 5.
MEDELLER: homology-based coordinate generation for membrane proteins.
Kelm S, Shi J, Deane CM.

iMembrane – Homology-Based Insertion of Proteins into the Membrane

iMembrane

:: DESCRIPTION

iMembrane is a homology-based method, which predicts a membrane protein’s position within a lipid bilayer. It projects the results of coarse-grained molecular dynamics simulations onto any membrane protein structure or sequence provided by the user.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
  • Java

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Apr 15;25(8):1086-8. doi: 10.1093/bioinformatics/btp102. Epub 2009 Feb 23.
iMembrane: homology-based membrane-insertion of proteins.
Kelm S, Shi J, Deane CM.

Aequatus – Open-source Homology Browser

Aequatus

:: DESCRIPTION

Aequatus is an open-source web-based tool to visualise homologous gene structures among differing species or subtypes of a common species.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser/ Linux

:: DOWNLOAD

Aequatus

:: MORE INFORMATION

Citation

Aequatus: an open-source homology browser.
Thanki AS, Soranzo N, Herrero J, Haerty W, Davey RP.
Gigascience. 2018 Nov 1;7(11). doi: 10.1093/gigascience/giy128.

PubServer – Literature Searches by Homology

PubServer

:: DESCRIPTION

PubServer collects homologous sequences from NR database and retrieves and filters associated publications.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W430-5. doi: 10.1093/nar/gku450. Epub 2014 Jun 23.
PubServer: literature searches by homology.
Jaroszewski L, Koska L, Sedova M, Godzik A

HHpred 3.2.0 – Protein Remote Homology Detection and 3D Structure Prediction

HHpred 3.2.0

:: DESCRIPTION

HHpred is a server for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs. In fact, HHpred’s sensitivity is competitive with the most powerful servers for structure prediction currently available.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

HHpred

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2015 Oct 23;11(10):e1004343. doi: 10.1371/journal.pcbi.1004343. eCollection 2015 Oct.
Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.
Meier A, Söding J.

HHblits 3.2.0 – Homology Detection by Iterative HMM-HMM Comparison

HHblits 3.2.0

:: DESCRIPTION

HHblits is the first iterative method based on the pairwise comparison of profile Hidden Markov Models. In benchmarks it achieves better runtimes than other iterative sequence search methods such as PSI-BLAST or HMMER3 by using a fast prefilter based on profile-profile comparison. Furthermore, HHblits greatly improves upon PSI-BLAST and HMMER3 in terms of sensitivity/selectivity and alignment quality.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

  Part of HH-suite

:: MORE INFORMATION

Citation

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Remmert M, Biegert A, Hauser A, Söding J.
Nat Methods. 2011 Dec 25;9(2):173-5. doi: 10.1038/nmeth.1818.

HMMER 3.2.1 – Protein Sequence Homology Search

HMMER 3.2.1

:: DESCRIPTION

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models Profile Hidden Markov Models for Sequence Analysis.

::DEVELOPER

Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

HMMER

:: MORE INFORMATION

Citation

HMMER web server: 2015 update.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR.
Nucleic Acids Res. 2015 May 5. pii: gkv397.

HMMER web server: interactive sequence similarity searching
R.D. Finn, J. Clements, S.R. Eddy
Nucl. Acids Res. (2011) 39 (suppl 2): W29-W37

R. Durbin, S. Eddy, A. Krogh, and G. Mitchison,
Biological sequence analysis: probabilistic models of proteins and nucleic acids,
Cambridge University Press, 1998.

M-Coffee – Combination of Multiple Sequence Alignment Packages

M-Coffee

:: DESCRIPTION

M-Coffee is a multiple sequence alignment Package. It is part of the T-Coffee distribution. The specificity of M-Coffee is that rather than computing a multiple sequence alignment on its own, it uses other packages to compute the alignments. It then uses T-Coffee to combine all these alignents into one unique final alignment.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Wallace IM, O’Sullivan O, Higgins DG, Notredame C.
Nucleic Acids Res. 2006 Mar 23;34(6):1692-9. Print 2006.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W645-8. Epub 2007 May 25.

DAPPLE 2 – Homology-based Prediction of Phosphorylation Sites

DAPPLE 2

:: DESCRIPTION

DAPPLE is a homology-based method for predicting phosphorylation sites in an organism of interest. It uses BLAST searches of experimentally-determined phosphorylation sites in one organism (or several organisms) to predict phosphorylation sites in an organism of interest. It outputs a table containing information helpful for choosing phosphorylation sites that are of interest to you, such as the number of sequence differences between the query site and the hit site, the location of the query site and the hit site in their respective intact proteins, and whether the corresponding intact proteins are reciprocal BLAST hits (and thus predicted orthologues).

::DEVELOPER

Bioinformatics Research Group, University of Saskatchewan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DAPPLE 2: a tool for the homology-based prediction of post-translational modification sites.
Trost B, Maleki F, Kusalik A, Napper S.
J Proteome Res. 2016 Jul 1.

Bioinformatics. 2013 Jul 1;29(13):1693-5. doi: 10.1093/bioinformatics/btt265. Epub 2013 May 8.
DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites.
Trost B, Arsenault R, Griebel P, Napper S, Kusalik A.