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.

Webservices


H2r

Tool to predict residues that are important for protein function based on correlated mutations.

CLIPS-1D

Tool to predict 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.

GCB4genome

Tool to predict translational efficiency for whole genomes.

GCB4gene

Tool to predict translational efficiency for single genes.

Software


CTRL-F

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

AGeNNT

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

ShortID

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

H2rs

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

PresCont

3D structures and MSAs for protein-protein complexes.

SIGI-HMM

Prediction of genomic islands.

YACOP

Enhanced meta gene-prediction tool.

Datasets


MSF

Benchmark datasets for Rosetta:MSF

BGC_KEGG

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

GO4genome

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