Computational Protein Design and Evolution


Team of Prof. Dr. Rainer Merkl

Our goal is the design and implementation of algorithms solving problems in computational biology. Main topics are related to protein evolution and the development of tools for protein design. In many cases, we utilise knowledge-based potentials deduced from large data sets. Have a look at our different web services, software packages, and datasets.

University of Regensburg About our group Contact

Webservices

H2r

Predicts residues that are important for protein function based on correlated mutations.

CLIPS-1D

Predicts functionally and structurally important residue-positions from 1D data.

CLIPS-4D

Tool to predict functionally and structurally important residue-positions from 1D and 3D data.

PresCont

Tool for the prediction of protein-protein interfaces.
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GCB4genome

Tool to predict translational efficiency for whole genomes.
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GCB4gene

Tool to predict translational efficiency for single genes.
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cSeqLogo

Generation of consensus referenced two-sample Sequence Logos.
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shortID

Generates taxonomic abbreviations from sequence accession numbers.
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Software

CTRL-F

Find amino acid sequences in PyMol like in your favourite browser; by pressing CTRL-F

GitHub

AGeNNT

Java program for the computation of refined genomic neighborhood networks (rGNNs).

Download

ShortID

Command line tool for replacing sequence database keys with a meaningful phylogenetic annotation.

GitHub

H2rs

Predicting residues important for protein function or structure based on the von Neumann entropy.

Download

PresCont

3D structures and MSAs for protein-protein complexes.
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Download

SIGI-HMM

Prediction of genomic islands.
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Uni Göttingen

YACOP

Enhanced meta gene-prediction tool.
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Uni Göttingen

Datasets

MSF

Benchmark datasets for Rosetta:MSF
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Download

BGC_KEGG

A set of html pages containing the genomic neighborhood of BLAST hits of Biosynthetic Gene Cluster.

Download

GO4genome

Whole genome phylogeny; source code and Y. pestis dataset.
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Source Code Y. pestis dataset