CPSP-Tools Server


This web server provides online access to a series of tools developed by the Freiburg Bioinformatics Group. To start using it, please select from the listings below, or use the menu on the left. If you prefer doing a local installation on your machine, please visit our 'Download' section.

If you use our tools for research or education, please cite the corresponding articles from the 'Publications' section.

Version 4.4.5

CPSP-Tools Server

CPSP (Constraint-based Protein Structure Prediction) is an exact and efficient approach to identify optimal structures of lattice proteins within the hydrophobic-polar (HP) model. The approach enables structure prediction within the 3D cubic and 3D face-centered-cubic (FCC) lattice for both backbone-only as well as side-chain representing models.

HPstruct implements the CPSP approach, as introduced by Backofen and Will (2006), to predict provably optimal structures of 3D lattice proteins in the HP-model. For a given HP-sequence and a given lattice type (cubic or face centered cubic), (all) optimal structures are calculated. The CPSP approach computes the global minimal energy for the input sequence.

HPview allows for the interactive visualization of lattice protein structures in the HP-model.

LatFit calculates a low deviation on-lattice model of a given full atom protein structure in Protein Data Base (PDB) format. It utilizes a greedy distance or coordinate RMSD optimizating approach while successively fitting the structures monomers on the lattice. It supports backbone-only and sidechain-including models within various lattices.

The Freiburg Bioinformatics Group also provides:

Freiburg RNA Tools

RNA Tools
Freiburg RNA tools provides online access to a series of RNA research tools developed by the Freiburg Bioinformatics Group and colleagues for sequence-structure alignments (LocARNA, CARNA, MARNA), clustering (ExpaRNA), interaction prediction (IntaRNA, CopraRNA, metaMIR), identification of homologs (GLASSgo), sequence design (AntaRNA, INFORNA, SECISDesign), CRISPR repeat analyses (CRISPRmap), and many more tasks.

MoDPepInt Server

MoDPepInt (Modular Domain Peptide Interaction) is a simple and interactive webserver, which comprises three different tools, i.e. SH2PepInt, SH3PepInt and PDZPepInt, for predicting the binding partners of three different modular protein domains, i.e. SH2, SH3 and PDZ domains, respectively.

Galaxy Project - Uni Freiburg

The Freiburg Galaxy Team offers a framework for scientists on e.g. NGS data analyses (RNA-seq, ChIP-seq, Exome-seq, MethylC-seq), genome annotation analyses for eukaryotic and prokaryotic organisms (from gene prediction to functional description), Proteomics and Metabolomics analysis, and the ChemicalToolBoX for analysis of small compounds. Galaxy contains more than 800 different single analysis tools and ready-to-use pipelines for different applications.

The Freiburg Galaxy Project is part of the “German Network for Bioinformatics Infrastructure” (Deutsches Netzwerk für Bioinformatik-Infrastruktur, de.NBI) and the Collaborative Research Centre (CRC) 992 for Medical Epigenetics and offers within the RNA Bioinformatic Centre (RBC) a central platform for RNA analysis.

CMV server

CMV server
CMV (co-variance model visualization) offers tools for the visualization of RNA family models, also known as co-variance models (CM) and Hidden Markov Models (HMM). Moreover, comparisons between models, the multiple sequence alignments they were constructed from and, in the case of RNA families, the consensus secondary structure can be visualized. The aim is to simplify model construction and evaluation by providing visualizations with different levels of detail.