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.

RateLimit – Rate Limiting Steps in Transcription from RNA production times in live cells

RateLimit

:: DESCRIPTION

RateLimit is a tool to identify rate limiting steps in transcription from RNA production times in live cells.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

RateLimit

:: MORE INFORMATION

Citation:

Häkkinen A, Ribeiro AS.
Characterizing rate limiting steps in transcription from RNA production times in live cells.
Bioinformatics. 2016 May 1;32(9):1346-52. doi: 10.1093/bioinformatics/btv744. Epub 2015 Dec 31. PMID: 26722120.

Adapt-A-Rate 1.0 – Estimate the Rate of Adaptive Fixation in Population

Adapt-A-Rate 1.0

:: DESCRIPTION

Adapt-A-Rate is a program to estimate the rate of adaptive fixation in a population from sequences sampled at different points in time.

::DEVELOPER

Samir Bhatt and Oliver Pybus

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Adapt-A-Rate

:: MORE INFORMATION

Citation:

Bhatt S, Holmes EC, Pybus OG (2011)
The genomic rate of molecular adaptation of the human influenza A virus.
Molecular Biology & Evolution In press

traitRate 201612 – Detection of Trait-dependent Shifts in the Rate of Sequence Evolution

traitRate 201612

:: DESCRIPTION

traitRate is a program for the detection of trait-dependent shifts in the rate of sequence evolution.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

  traitRate

:: MORE INFORMATION

Citation

Mayrose I and Otto SP. 2011.
A Likelihood Method for Detecting Trait-Dependent Shifts in the Rate of Molecular Evolution.
Mol Biol Evol. 28:781-791.

SeqRate 1.0 – Sequence-based Prediction of Protein Folding rates

SeqRate 1.0

:: DESCRIPTION

SeqRate is a software to predict both protein folding kinetic type (two-state versus multi-state) and real-value folding rate using sequence length, amino acid composition, contact order, contact number, and secondary structure information predicted from only protein sequence with support vector machines.

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SeqRate

:: MORE INFORMATION

Citation

Guanning Lin, Zheng Wang, Dong Xu, and Jianlin Cheng.
SeqRate: Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structure and Support Vector Machines.
BMC Bioinformatics. 11(S3):S1, 2010.