PEAT / PEATDB 2.3 / PEATSA – Protein Engineering Analysis Tool

PEAT / PEATDB 2.3 / PEATSA

:: DESCRIPTION

PEAT is a collection of software that aids researchers in the field of protein analysis, engineering and design.

PEATDB (Protein Engineering Analysis Tool – Database) is a workbench for protein studies that provides some of the functions of a Laboratory Information Management System (LIMS) integrated with analysis tools.

PEATSA (Protein Engineering Analysis Tool – Structure Analysisis) a part of the PEAT suite of programs for storing, analysing and predicting biophysical data on proteins

::DEVELOPER

PEAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / Mac OsX
Python

:: DOWNLOAD

PEAT

:: MORE INFORMATION

Citation

Proteins. 2011 Jan;79(1):165-78. doi: 10.1002/prot.22870.
Integrated prediction of the effect of mutations on multiple protein characteristics.
Johnston MA1, Søndergaard CR, Nielsen JE.

Proteins: From Birth to Death 21st Annual Symposium of The Protein Society, July 21-25, 2007, Boston, MA, USA
Georgi N, Farrell D, O’Meara F, Webb H, Tynan-Connolly BM, Bjarnadottir U, Soendergaard C, Nielsen JE
Structural analysis of datasets from protein engineering studies using PEAT

VisualCNA 1.0 – Constraint Network Analysis and Protein Engineering

VisualCNA 1.0

:: DESCRIPTION

VisualCNA is a PyMOL plug-in for interactive Constraint Network Analysis and protein engineering for improving thermostability

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows/MacOsX
Python
PyMOL

:: DOWNLOAD

VisualCNA

:: MORE INFORMATION

Citation

VisualCNA: A GUI for interactive Constraint Network Analysis and protein engineering for improving thermostability.
Rathi PC, Mulnaes D, Gohlke H.
Bioinformatics. 2015 Mar 12. pii: btv139.

HotSpot Wizard 3.0 – Identification of Hot Spots in Protein Engineering

HotSpot Wizard 3.0

:: DESCRIPTION

HotSpot Wizard is a web server for automatic identification of ‘hot spots’ for engineering of substrate specificity, activity or enantioselectivity of enzymes and for annotation of protein structures.

::DEVELOPER

Protein Engineering Group, Loschmidt Laboratories

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information.
Sumbalova L, Stourac J, Martinek T, Bednar D, Damborsky J.
Nucleic Acids Res. 2018 Jul 2;46(W1):W356-W362. doi: 10.1093/nar/gky417.

HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering.
Bendl J, Stourac J, Sebestova E, Vavra O, Musil M, Brezovsky J, Damborsky J.
Nucleic Acids Res. 2016 May 12. pii: gkw416.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W376-83. doi: 10.1093/nar/gkp410. Epub 2009 May 21.
HotSpot Wizard: a web server for identification of hot spots in protein engineering.
Pavelka A1, Chovancova E, Damborsky J.

myPresto 5.000 / omegagene 0.38 – Medicinally Yielding PRotein Engineering SimulaTOr

myPresto 5.000 / omegagene 0.38

:: DESCRIPTION

myPresto is a program suite composed of several molecular simulations for drug development.

myPresto/omegagene is a Molecular Dynamics Simulation Engine.

::DEVELOPER

myPresto team

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

myPresto

:: MORE INFORMATION

Citation

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.
Kasahara K, Ma B, Goto K, Dasgupta B, Higo J, Fukuda I, Mashimo T, Akiyama Y, Nakamura H.
Biophys Physicobiol. 2016 Sep 7;13:209-216.

TRITON 4.0 – Computational Aided Protein Engineering.

TRITON 4.0

:: DESCRIPTION

TRITON is a graphical tool for computational aided protein engineering.It implements methodology of computational site-directed mutagenesis to design new protein mutants with required properties. It uses the external program MODELLER to model structures of new protein mutants based on the wild-type structure by homology modelling method.

::DEVELOPER

NCBR

:: SCREENSHOTS

:: REQUIREMENTS

Linux

:: DOWNLOAD

TRITON

:: MORE INFORMATION

Citation:

Prokop, M., Adam, J., Kriz, Z., Wimmerova, M., Koca, J. 2008:
TRITON: a graphical tool for ligand-binding protein engineering
Bioinformatics 24: 1955-1956.