SWISS-MODEL – Protein Structure Homology-modelling Server

SWISS-MODEL

:: DESCRIPTION

SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).

::DEVELOPER

Protein Structure Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W252-8. doi: 10.1093/nar/gku340. Epub 2014 Apr 29.

SPANNER 1.0.0 – Homology-based Taxonomic Classification of Protein Sequences

SPANNER 1.0.0

:: DESCRIPTION

SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • C++ Compiler
  • Python

:: DOWNLOAD

 SPANNER

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1858-64. doi: 10.1093/bioinformatics/btt313.
SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles.
Porter MS, Beiko RG.

CopraRNA 2.1.3 – sRNA Target Prediction utilizing Homology

CopraRNA 2.1.3

:: DESCRIPTION

CopraRNA (Comparative Prediction Algorithm for sRNA Targets) is a tool for sRNA target prediction. It computes whole genome predictions by combination of distinct whole genome IntaRNA predictions. As input, CopraRNA requires at least 3 homologous sRNA sequences from 3 distinct organisms in FASTA format.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CopraRNA 

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):E3487-96. doi: 10.1073/pnas.1303248110. Epub 2013 Aug 26.
Comparative genomics boosts target prediction for bacterial small RNAs.
Wright PR1, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J.

Jali 1.3 – Remote Homology Detection for Protein

Jali 1.3

:: DESCRIPTION

Jali (Jumping Alignments) is an alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Watherman algorithm.

::DEVELOPER

Jens Stoye

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Jali

:: MORE INFORMATION

Citation

A novel approach to remote homology detection: Jumping Alignments
R. Spang, M. Rehmsmeier, J. Stoye
J. Comp. Biol., volume 9, pp. 747-760, 2002

CPHmodels 3.2 – Protein Homology Modeling server

CPHmodels 3.2

:: DESCRIPTION

CPHmodels is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Send inquiries by e-mail to software@cbs.dtu.dk.

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W576-81. doi: 10.1093/nar/gkq535. Epub 2010 Jun 11.
CPHmodels-3.0–remote homology modeling using structure-guided sequence profiles.
Nielsen M1, Lundegaard C, Lund O, Petersen TN.

MolIDE 1.7 – Protein 3D Homology Modeling

MolIDE 1.7

:: DESCRIPTION

MolIDE is an open-source cross-platform graphical environment for homology modeling. It implements the most frequently used steps involved in modeling: sequence search, secondary structure prediction, multiple-round psiblast alignments, assisted alignment editing (integrating a template viewer and secondary structure prediction), side chain replacement and loop building. MolIDE takes an input target sequence and uses PSIBLAST to identify and align templates for comparative modeling of the target. The sequence alignment to any template can be manually modified within a graphical window of the target–template alignment and visualization of the alignment on the template structure. MolIDE builds the model of the target structure on the basis of the template backbone, predicted side.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux
  • SCWRL

:: DOWNLOAD

MolIDE

:: MORE INFORMATION

Citation

Qiang Wang, Adrian A Canutescu & Roland L Dunbrack Jr
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling
Nature Protocols 3:1832-1847 (2008)

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.