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Höcker lab – Protein Design

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Algorithms & Software

ProteinToolsHide

ProteinTools: A toolkit for protein structural analysis

ProteinTools is a web server for the analysis of different structural properties in proteins. It is possible to analyze hydrophobic clusters, hydrogen bond networks, salt bridges, and contact maps, in an easy to use interactive interface.

Ferruz et al., 2021

ProteinTools is accessible here: https://proteintools.uni-bayreuth.de

ProtlegoHide

Protlego for the automatic design of chimeras and their analysis

Protlego is a tool that enables constructing protein chimeras and its structural analysis. ProtLego is written in Python, so it facilitates that other scientists can extend it to their needs.

With Protlego, it is possible to go from a pair of PDBs that share a structural fragment in common, to build all possible chimeras between the two, rank them with the AMBER or CHARMM molecular mechanics forcefields, and analyze their structural features (hydrogen networks, salt bridges, hydrophobic clusters…etc.)

Ferruz et al., 2021

Accessible here: https://hoecker-lab.github.io/protlego

FuzzleHide

Fuzzle: A web resource to identify and analyze natural protein building blocks

Proteins have evolved by replicating and recombining sub-domain-sized fragments. By using super-sensitive homology detection tools, we have identified over 1000 fragments that appear across the protein space. These fragments can be used as building blocks to construct novel proteins, mimicking the natural process. We have made these data available in our Fuzzle database:

Ferruz et al., 2020 & Ferruz et al., 2021

Accessible here: https://fuzzle.uni-bayreuth.de/2.0

PocketOptimizerHide

prediction of affinity increasing mutations in a protein-binding pocket

Malisi et al., 2012

Version 1.2.0 - March 2016

Dependencies: all dependencies included except for python 2.7, numpy, tinker and matplotlib.
Providing binaries for Linux 64bit only

src

Linux x86_64

Dockerfile for installing automatically as Docker Container

Version 1.1.0 - March 2014

Dependencies: all dependencies included except for python 2.7.6, numpy, and matplotlib.
Providing binaries for Linux, Windows, and OS X

src

Linux x86_64

Windows i386

OS X 10.9 x86_64

OS X 10.9 i386

OS X 10.6 x86_64

OS X 10.6 i386

Version 1.0 - October 2009

Dependencies: BALL

src

ScaffoldSelectionHide

searches large sets of protein structures for potential attachment sites of an enzymatic motif

Malisi et al., 2009

Version 1.2.0 - February 2014

Dependencies: all dependencies included
Providing binaries for Linux, Windows, and OS X (incl. BALL & boost)

src

Linux x86_64

Windows i386

OS X 10.9 x86_64

OS X 10.9 i386

OS X 10.6 x86_64

OS X 10.6 i386

Version 1.1.0 - December 2013

Dependencies: BALL 1.4.2, boost 1.55, lpsolve 5.5
Binary version for Linux

src

Linux x86_64

Version 1.0 - October 2009

Dependencies: BALL 1.2, boost 1.55, lpsolve 5.5

src


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