iRefIndex 14 / iRefScape 1.18 / iRefR 1.13 – Downloading Consolidated Protein Interaction data and Visualization

iRefIndex 14 / iRefScape 1.18 / iRefR 1.13

:: DESCRIPTION

iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI and OPHID.

iRefScape is a plugin for Cytoscape that exposes iRefIndex data as a navigable graphical network.

iRefR is an R package that provides access to iRefIndex.

::DEVELOPER

Donaldson Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package / Cytoscape / Matlab
  • Java

:: DOWNLOAD

 iRefIndex / iRefScape / iRefR

:: MORE INFORMATION

Citation

iRefIndex: a consolidated protein interaction database with provenance.
Razick S, Magklaras G, Donaldson IM.
BMC Bioinformatics. 2008 Sep 30;9:405.

BMC Bioinformatics. 2011 Oct 5;12:388.
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex.
Razick S, Mora A, Michalickova K, Boddie P, Donaldson IM.

Antonio Mora and Ian M Donaldson
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database.
BMC Bioinformatics 2011, 12:455

GraphiteLifeExplorer 20120731 – Model in 3D Assemblies of Proteins and DNA

Graphite-LifeExplorer 20120731

:: DESCRIPTION

GraphiteLifeExplorer (G-LE,  former Graphite-MicroMégas) is a software for the building and visualization of macromolecular assemblies. Its main feature is the capability to create (and export) 3D models of DNA in a highly intuitive manner.

::DEVELOPER

Samuel Hornus

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  GraphiteLifeExplorer

:: MORE INFORMATION

Citation

Easy DNA modeling and more with GraphiteLifeExplorer
Samuel Hornus, Bruno Levy, Damien Larivière, Eric Fourmentin
Research article published 07 Jan 2013 PLOS ONE

NIAS-Server 1.0 – Neighbors Influence of Amino acids and Secondary Structures in Proteins

NIAS-Server 1.0

:: DESCRIPTION

NIAS is a server to help the analysis of the conformational preferences of amino acid residues in proteins.

::DEVELOPER

SBCB – Structural Bioinformatics and Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins.
Borguesan B, Inostroza-Ponta M, Dorn M.
J Comput Biol. 2016 Aug 5.

SolubiS 1.0 – Optimize your protein

SolubiS 1.0

:: DESCRIPTION

SolubiS is a method to identify stabilizing mutations that reduce the aggregation tendency of a protein.

The Solubis plugin for YASARA is a software package to identify mutants that decrease the aggregation tendency with YASARA. This package combines TANGO, FoldX and YASARA.

::DEVELOPER

Switch Laboratory

:: SCREENSHOTS

Solubis

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • YASARA

:: DOWNLOAD

 Solubis

:: MORE INFORMATION

Citation

Solubis: a webserver to reduce protein aggregation through mutation.
Van Durme J, De Baets G, Van Der Kant R, Ramakers M, Ganesan A, Wilkinson H, Gallardo R, Rousseau F, Schymkowitz J.
Protein Eng Des Sel. 2016 Jun 9. pii: gzw019.

Solubis: Optimize your protein.
De Baets G, Van Durme J, van der Kant R, Schymkowitz J, Rousseau F.
Bioinformatics. 2015 Mar 19. pii: btv162.

FRAGSION 1.0 – Protein Fragment Library Generation

FRAGSION 1.0

:: DESCRIPTION

FRAGSION is a database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model.

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 FRAGSION

:: MORE INFORMATION

Citation

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.
Bhattacharya D, Adhikari B, Li J, Cheng J.
Bioinformatics. 2016 Feb 18. pii: btw067

SMOQ 1.0 – Protein Single Model Local Quality Prediction

SMOQ 1.0

:: DESCRIPTION

SMOQ is a tool for protein single model local quality prediction

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SMOQ

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Apr 28;15:120. doi: 10.1186/1471-2105-15-120.
SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines.
Cao R, Wang Z, Wang Y, Cheng J

SVMcon 1.0 – Protein Contact Map Prediction using Support Vector Machine

SVMcon 1.0

:: DESCRIPTION

SVMcon predicts medium- to long-range residue-residue contacts using Support Vector Machines. The contact predictions are in the CASP format (residue index 1, residue index 2, 0, 8, contact probability). The contact distance threshold is 8 angstrom. The sequence separation between two residues is at least 6 residues.

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SVMcon

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Apr 2;8:113.
Improved residue contact prediction using support vector machines and a large feature set.
Cheng J, Baldi P.

i3Drefine / 3Drefine – Protein 3D Structure Refinement

i3Drefine / 3Drefine

:: DESCRIPTION

i3Drefine is a completely automated and computationally efficient protein 3D structure refinement method which based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique.

3Drefine: protein structure refinement server

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 i3Drefine

:: MORE INFORMATION

Citation

3Drefine: an interactive web server for efficient protein structure refinement.
Bhattacharya D, Nowotny J, Cao R, Cheng J.
Nucleic Acids Res. 2016 Apr 29. pii: gkw336

3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization.
Bhattacharya D, Cheng J.
Proteins. 2013 Jan;81(1):119-31. doi: 10.1002/prot.24167.

PLoS One. 2013 Jul 19;8(7):e69648. doi: 10.1371/journal.pone.0069648. Print 2013.
i3Drefine software for protein 3D structure refinement and its assessment in CASP10.
Bhattacharya D1, Cheng J.

MULTICOM / MULTICOM Toolbox – Protein Tertiary Structure Prediction

MULTICOM / MULTICOM Toolbox

:: DESCRIPTION

MULTICOM is a protein tertiary structure predictor using multi-template combination

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MULTICOM Toolbox

:: MORE INFORMATION

Citation

Z. Wang, J. Eickholt, and J. Cheng.
MULTICOM: A Multi-Level Combination Approach to Protein Structure Prediction and its Assessment in CASP8.
Bioinformatics. 26(7):882-888, 2010.

Large-scale model quality assessment for improving protein tertiary structure prediction.
Cao R, Bhattacharya D, Adhikari B, Li J, Cheng J.
Bioinformatics. 2015 Jun 15;31(12):i116-i123. doi: 10.1093/bioinformatics/btv235.

SubLoc 1.0 – Prediction of Protein Subcellular Localization

SubLoc 1.0

:: DESCRIPTION

SubLoc is a prediction system for protein subcellular localization based on amino acid composition alone.

::DEVELOPER

Sun Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SubLoc: a server/client suite for protein subcellular location based on SOAP.
Chen H, Huang N, Sun Z.
Bioinformatics. 2006 Feb 1;22(3):376-7.