FEATURE 3.1 – Examine Biological Structures

FEATURE 3.1

:: DESCRIPTION

FEATURE is an automated tools that examines biological structures and produces useful representations of the key biophysical and biochemical features of these structures that are critical for understanding function. The utility of this system extends from medical/pharmaceutical applications (model-based drug design, comparing pharmacological activities) to industrial applications (understanding structural stability, protein engineering).

::DEVELOPER

FEATURE Team

:: SCREENSHOTS

 

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 FEATURE

:: MORE INFORMATION

Citation:

Halperin I, Glazer DS, Wu S, Altman RB.
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications.”
BMC Genomics. 9 Suppl 2 S2.

HiTRACE 2.2.0 / HiTRACE-Web – High-Throughput Robust Analysis for Capillary Electrophoresis

HiTRACE 2.2.0 / HiTRACE-Web

:: DESCRIPTION

HiTRACE is a suite of robust and efficient analysis software to facilitate the analysis of large-scale high-throughput CE data.It has been intensively used for quantitating data for RNA and DNA based on the mutate-and-map methodology, chromatin footprinting, and other high-throughput structure mapping techniques.

HiTRACE-Web is an online version of HiTRACE that presents both standard features previously available only in the MATLAB environment as well as additional features such as automated band annotation and flexible adjustment of annotations, all via an integrative, user-friendly, and interactive environment.

::DEVELOPER

Das Lab , Seoul National University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX/ Windows
  • MatLab

:: DOWNLOAD

 HiTRACE

:: MORE INFORMATION

Citation

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis.
Kim H, Cordero P, Das R, Yoon S.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W492-8. doi: 10.1093/nar/gkt501.

HiTRACE: high-throughput robust analysis for capillary electrophoresis.
Yoon S, Kim J, Hum J, Kim H, Park S, Kladwang W, Das R.
Bioinformatics. 2011 Jul 1;27(13):1798-805. doi: 10.1093/bioinformatics/btr277

SOLart 1.0 – Protein Solubility Prediction

SOLart 1.0

:: DESCRIPTION

SOLart is a fast and accurate method for predicting the protein solubility of a target protein whose experimental or modeled structure is available. It yields a scaled solubility score with values close to zero indicating aggregate-prone proteins, while values close to 130 designate soluble proteins.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics, 36 (5), 1445-1452 2020 Mar 1
SOLart: A Structure-Based Method to Predict Protein Solubility and Aggregation
Qingzhen Hou , Jean Marc Kwasigroch, Marianne Rooman, Fabrizio Pucci

SCooP 1.0 – Prediction of the Stability Curve of Proteins

SCooP 1.0

:: DESCRIPTION

SCooP is a fast and accurate method for predicting the Gibbs-Helmholtz equation associated to the folding transition of a target protein of known (or modeled) structure. In addition, SCooP yields an estimation of the thermodynamic quantities that characterize the folding process, in particular the change in enthalpy and in heat capacity upon folding, the melting temperature and the folding free energy at room temperature.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

F. Pucci, J.M. Kwasigroch, M. Rooman (2017),
SCooP : an accurate and fast predictor of protein stability curves as a function of the temperature,
Bioinformatics 33, 3415-3422.

WholeCellViz – Data Visualization for Whole-cell Models

WholeCellViz

:: DESCRIPTION

WholeCellViz is a web-based software program for visually analyzing whole-cell simulations.

::DEVELOPER

Karr Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

WholeCellViz

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 21;14:253. doi: 10.1186/1471-2105-14-253.
WholeCellViz: data visualization for whole-cell models.
Lee R1, Karr JR, Covert MW.

iFBA 1.0 – Integrated Flux Balance Analysis Model of Escherichia coli

iFBA 1.0

:: DESCRIPTION

iFBA (Integrated Flux Balance Analysis Model of Escherichia coli) includes several MATLAB scripts that simulate E. coli central metabolism and the effects of single gene deletions on metabolism using 3 approaches — iFBA, rFBA, and ODE. The project also includes several MATLAB scripts that simulate biochemical networks using 1) integrated flux balance analysis (iFBA) — a combined FBA, boolean regulatory, and ODE approach; 2) regulatory flux balance analysis (rFBA); and 3) ordinary differential equations (ODE). Additionally, the project includes several MATLAB and php scripts for visualizing metabolic simulations.

::DEVELOPER

Covert Systems Biology Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • MATLAB

:: DOWNLOAD

 iFBA

:: MORE INFORMATION

Citation:

Covert, M.W., Xiao, N., Chen, T.J., and Karr, J.R. (2008)
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
Bioinformatics. 24(18): 2044-2050.

NetPhorest 2.1 – Model Phosphorylation driven Cellular Signaling Networks

NetPhorest 2.1

:: DESCRIPTION

NetPhorest integrates in vitro kinase and phosphopeptide-binding domain specificity assays with publically accessible known in vivo substrate lists in order to generate substrate specificity descriptions for individual proteins as well as protein families.

::DEVELOPER

NetPhorest team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 NetPhorest

:: MORE INFORMATION

Citation

Miller et al.,
Linear Motif Atlas for Phosphorylation-Dependent Signaling.
Science Signaling, 2 September 2008, Vol 1, Issue 35, p. ra2.

BeAtMuSiC 1.0 – Prediction of Binding Affinity Changes upon Mutations

BeAtMuSiC 1.0

:: DESCRIPTION

The BeAtMuSiC program evaluates the change in binding affinity between proteins (or protein chains) caused by single-site mutations in their sequence.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W333-9. doi: 10.1093/nar/gkt450. Epub 2013 May 30.
BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations.
Dehouck Y, Kwasigroch JM, Rooman M, Gilis D.

SODa – SuperOxide Dismutase Annotation Tool

SODa

:: DESCRIPTION

The SODa webtool predicts if a target sequence corresponds to an Fe/Mn Superoxide dismutases (SODs) .

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Jun 2;9:257. doi: 10.1186/1471-2105-9-257.
SODa: an Mn/Fe superoxide dismutase prediction and design server.
Kwasigroch JM1, Wintjens R, Gilis D, Rooman M.

Autoosc 0.1 – Automated Analysis of Biological Oscillator Models using Mode Decomposition

Autoosc 0.1

:: DESCRIPTION

Autoosc is a Mathematica package for analyzing time-series of oscillatory signals, particularly those originating from biological/chemical systems.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Mathematica

:: DOWNLOAD

  Autoosc

:: MORE INFORMATION

Citation

Automated analysis of biological oscillator models using mode decomposition.
Konopka T.
Bioinformatics. 2011 Apr 1;27(7):961-7. doi: 10.1093/bioinformatics/btr069