ELASPIC – Ensemble Learning Approach for Stability Prediction of Interface and Core Mutations

ELASPIC

:: DESCRIPTION

ELASPIC constructs homology models of domains and domain-domain interactions, and uses those models, together with sequential and other features, to predict the energetic impact of a mutation on the stability of a single domain or the affinity between two domains.

::DEVELOPER

Kim Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ELASPIC web-server: proteome-wide structure based prediction of mutation effects on protein stability and binding affinity.
Witvliet D, Strokach A, Giraldo-Forero AF, Teyra J, Colak R, Kim PM.
Bioinformatics. 2016 Jan 21. pii: btw031.

 

PDIviz 1.1 – Visualization of Protein-DNA Binding Interfaces

PDIviz 1.1

:: DESCRIPTION

PDIviz is a plugin for the PyMOL molecular visualization system that is specifically designed to visualize protein-DNA interfaces in three dimensions. PDIviz detects the interface of protein-DNA complexes by calculating the buried surface area directly in PyMOL.

::DEVELOPER

MBL – Laboratorio de Bioinformática

:: SCREENSHOTS

PDIviz

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python
  • PyMOL

:: DOWNLOAD

  PDIviz

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Apr 16. pii: btv203.
PDIviz: Analysis and visualization of protein-DNA binding interfaces.
Ribeiro J, Melo F, Schüller A

RamiGO 1.16.0 – AmiGO Visualization Interface for R

RamiGO 1.16.0

:: DESCRIPTION

RamiGO is an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

 RamiGO

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Mar 1;29(5):666-8. doi: 10.1093/bioinformatics/bts708. Epub 2013 Jan 6.
RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.
Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B.

CPORT – Prediction of Protein-protein Interface Residues

CPORT

:: DESCRIPTION

CPORT is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2011 Mar 25;6(3):e17695. doi: 10.1371/journal.pone.0017695.
CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.
de Vries SJ1, Bonvin AM.

visPIG 1.1 – Visual Plotting Interface for Genetics

visPIG 1.1

:: DESCRIPTION

visPIG is a web application to produce multi-track, multi-scale, multi-region plots of genetic data.

::DEVELOPER

Marc Henrion

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ MacOsX/Linux
  • R

:: DOWNLOAD

  visPIG

:: MORE INFORMATION

Citation:

visPIG–a web tool for producing multi-region, multi-track, multi-scale plots of genetic data.
Scales M, Jäger R, Migliorini G, Houlston RS, Henrion MY.
PLoS One. 2014 Sep 10;9(9):e107497. doi: 10.1371/journal.pone.0107497. eCollection 2014.

ICeE 2.10 – Interface for C. Elegans Experiments

ICeE 2.10

:: DESCRIPTION

ICeE is a database with a Web-browser interface that allows you to enter experiments for the nematode C. elegans and to search efficiently in this database.

::DEVELOPER

the Ewbank lab

:: SCREENSHOTS

ICeE

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Apache httpd
  • MySQL
  • PHP

:: DOWNLOAD

 ICeE

:: MORE INFORMATION

SketchBio 0.0.10 – 3D Interface for Molecular Modeling and Animation

SketchBio 0.0.10

:: DESCRIPTION

SketchBio is  a tool that incorporates state-of-the-art bimanual interaction and drop shadowsto enable rapid construction of molecular structures and animations

::DEVELOPER

CISMM (Computer Integrated Systems for Microscopy and Manipulation)

:: SCREENSHOTS

SketchBio

:: REQUIREMENTS

  • Windows
  • UCSF Chimera
  • Blender

:: DOWNLOAD

 SketchBio

 :: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Oct 30;15(1):334.
SketchBio: a scientist’s 3D interface for molecular modeling and animation.
Waldon SM, Thompson PM, Hahn PJ, Taylor RM 2nd.

MolSurfer 1.2 – a Macromolecular Interface Navigator

MolSurfer 1.2

:: DESCRIPTION

MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures.

:: DEVELOPER

Rebecca C. Wade

:: SCREENSHOTS

MolSurfer

:: REQUIREMENTS

  •  Linux /Windows/ MacOsX
  • Java

:: DOWNLOAD

 MolSurfer

:: MORE INFORMATION

Citation

Gabdoulline,R.R., Wade,R.C. and Walter,D.
MolSurfer: a macromolecular interface navigator
Nucl.Acid.Res. (2003) 31, 3349-3351.

MADIBA – MicroArray Data Interface for Biological Annotation

MADIBA

:: DESCRIPTION

MADIBA is a web interface for functional analysis of cluster of genes with same profile of expression for Plasmodium falciparum, Oryza Sativa (rice), Arabidopsis thaliana and Pectobacterium atrosepticum

::DEVELOPER

the Bioinformatics and Computational Biology Unit at the University of Pretoria

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Law PJ, Claudel-Renard C, Joubert F, Louw AI and Berger DK (2008)
MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters
BMC Genomics 9:105

PyRosetta 2.012 – Python-based Interface to Rosetta Molecular Modeling Suite

PyRosetta 2.012

:: DESCRIPTION

PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables a user to create custom molecular modeling algorithms with Rosetta sampling and scoring functions using Python scripting. PyRosetta is designed to make the sophisticated Rosetta molecular modeling suite accessible to a broader audience of scientists in the life sciences.

::DEVELOPER

the Gray Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

PyRosetta

:: MORE INFORMATION

Citation

S. Chaudhury, S. Lyskov & J. J. Gray,
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta,
Bioinformatics, 26(5), 689-691 (2010).