K-Fold – Predictor of the Protein Folding Mechanism and Rate

K-Fold

:: DESCRIPTION

K-Fold is a tool for the automatic prediction of the protein folding kinetic order and rate. The tool is based on a support vector machine (SVM) that was trained on a data set of 63 proteins, whose 3D structure and folding mechanism are known from experiments already described in the literature.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No, Only Web Service

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Feb 1;23(3):385-6. Epub 2006 Nov 30.
K-Fold: a tool for the prediction of the protein folding kinetic order and rate.
Capriotti E, Casadio R.

CHAIN 1.0.0 – Forging Evolutionary Links to Underlying Mechanisms

CHAIN 1.0.0

:: DESCRIPTION

Many important principles underlying how protein molecular machines work lie beyond the pale of direct experimental observation. CHAIN (Contrast Hierarchical Alignment and Interaction Network )  analysis is a statistical solution to this problem that follows Mendel’s example: Just as Mendel inferred principles underlying genetic mechanisms from observed patterns of inherited traits, CHAIN analysis seeks to infer principles underlying molecular mechanisms from observed patterns in protein sequences—the cell’s own language for encoding those mechanisms.

::DEVELOPER

Andrew F. Neuwald, Ph.D.

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CHAIN

:: MORE INFORMATION

Citation

Trends Biochem Sci. 2007 Nov;32(11):487-93. Epub 2007 Oct 24.
The CHAIN program: forging evolutionary links to underlying mechanisms.
Neuwald AF

ARN – Studying the Mechanism and Regulation of Autophagy

ARN

:: DESCRIPTION

ARN(Autophagy Regulatory Network) is an integrated resource to analyze regulatory network of autophagy proteins

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Autophagy. 2015;11(1):155-65. doi: 10.4161/15548627.2014.994346.
Autophagy Regulatory Network – a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy.
Türei D1,et al.

EvoDots 1.1 – Explore the Mechanism of Evolution

EvoDots 1.1

:: DESCRIPTION

EvoDots lets the user explore the mechanism of evolution. The program creates a population of dots. The user is a predator. As the dots run around the screen, the user eats them by clicking on them with the mouse. After the user has eaten some of the dots, the survivors will reproduce. The population may or may note evolve, depending on the properties of the dots.

::DEVELOPER

Jon C. Herron

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Windows 

:: DOWNLOAD

 EvoDots

:: MORE INFORMATION

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