Tag: Protein Folding

ProtEvol 1.0 – Maximum Likelihood Phylogenetic Inference with Selection on Protein Folding Stability

ProtEvol 1.0

:: DESCRIPTION

The program ProtEvol performs two kinds of computation.

  1. It computes the mean-field site-specific amino acid distributions that have minimal differences with respect to the background distribution and that constraint the average stability of the native state of the protein against both unfolding and misfolding. The program also computes an exchangeability matrix derived from an empirical substitution model or from a mutation model that can be used together with the site-specific distributions for applications in phylogenetic inference.
  2. It simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding.

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  ProtEvol

:: MORE INFORMATION

Citation

Maximum likelihood phylogenetic inference with selection on protein folding stability.
Arenas M, Sánchez-Cobos A, Bastolla U.
Mol Biol Evol. 2015 Apr 2. pii: msv085.

Protein Investigator 3.0.2 – Simulation of Protein Folding

Protein Investigator 3.0.2

:: DESCRIPTION

Protein Investigator gives students an opportunity to interactively explore protein structure and function in a simplified system. This is a highly-simplified model of protein folding. It is not intended to predict the correct structures of any proteins; it is designed to illustrate the major principles involved in that process.

::DEVELOPER

Brian White

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

Protein Investigator

:: MORE INFORMATION

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.

Foldit 20210811 – Solve Puzzles for Protein Folding

Foldit 20210811

:: DESCRIPTION

FoldIt is an online game in which humans try to solve one of the hardest computational problems in biology: protein folding. You don’t need to know anything about biology to play the game, although a little background will help. Most of the players of foldit are not biologists.

::DEVELOPER

Foldit Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

Foldit

:: MORE INFORMATION

Folding@home 7.6.21 – Understand Protein Folding, Misfolding & Related Diseases

Folding@home 7.6.21

:: DESCRIPTION

Folding@home is a distributed computing project — people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. Folding@home’goal is to understand protein folding, misfolding, and related diseases

::DEVELOPER

Folding@home Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX / PlayStation3 /Android

:: DOWNLOAD

Folding@home

:: MORE INFORMATION

Rosetta@home 3.65 – Grid Software for Protein Folding

Rosetta@home 3.65

:: DESCRIPTION

Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s.

::DEVELOPER

The Baker Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • BOINC

:: DOWNLOAD

BOINC (enter the project URL: http://boinc.bakerlab.org/rosetta)

:: MORE INFORMATION

UniCon3D 1.0 – United-residue Protein Folding via Stepwise, Probabilistic Sampling

UniCon3D 1.0

:: DESCRIPTION

UniCon3D is a software for de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling.

::DEVELOPER

Dr. Jianlin Cheng’

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 UniCon3D

:: MORE INFORMATION

Citation

UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling.
Bhattacharya D, Cao R, Cheng J.
Bioinformatics. 2016 Jun 3. pii: btw316

PconsFold v1.0 – Pipeline for Protein Folding using PconsC and Rosetta

PconsFold v1.0

:: DESCRIPTION

PconsFold is a pipeline for protein folding using predicted contacts from PconsC and a Rosetta folding protocol.

::DEVELOPER

Elofsson Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python
  • PconsC

:: DOWNLOAD

 PconsFold

:: MORE INFORMATION

Citation

PconsFold: improved contact predictions improve protein models.
Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A.
Bioinformatics. 2014 Sep 1;30(17):i482-i488. doi: 10.1093/bioinformatics/btu458.

P3Fold – Predicting Protein Folding Routes

P3Fold

:: DESCRIPTION

P3Fold is a protein folding pathway prediction framework that combines ensemble modelling techniques with evolutionary sequence information method.

::DEVELOPER

Computer Science and Biology at McGill

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

N/A

:: MORE INFORMATION

Citation:

Bioinformatics. 2019 Oct 4. pii: btz743. doi: 10.1093/bioinformatics/btz743.
Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation.
Becerra D, Butyaev A, Waldispühl J.

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.