PROTEIN MODELLING
PROTEIN ANALYSIS
DNA

The following page contains links to a number of bioinformatic tools, which i find useful. For our own tools check

the following link.

directed.evolution.group bioinformatics tools :

 

Useful.links
 
mFold :: Oligo Analyzer
M.Zucker's oligo nucleotide analyzer, calculate primer melting temperatures, check for dimers and hairpins
to optimize the primer design
 
LigationCalculator
calculate vector:insert molar ratio, based on vector and insert size
 
Insilco experiments with complete genomes
in silico PCR amplification on complete genomes, PCR.-RFLP, T-RFLP, DNA fingerprinting etc.

Molbio.ru :: molcular calculations, unit convertions  
convert  µg to µmol for DNA, proteins,
 
The Sequence Manipulation Suite
many DNA related tools, codon usage calculation, CpG island search, convert Genbank to FASTA format, but also
protein related tools: ORF finder, DNA translation etc ...
 
BCM Search Launcher::Promotor Prediction
predict promotor and transcription factore binding sites, prokaryotes, eukaryotes also exon, intron and gene model
prediction
 
Bioinformatics.Net
useful collection of online tools related to molecular biology
 
 
DNA translation for publication
translate DNA to protein in any given frame in a nice presentable manner
 
ClustalW :: alignments
Multiple sequence alignment tool, with output file generation (*.aln) for further use in e.g.GeneDoc, TreeView etc.
 
BoxShade :: Server
for pretty printing and shading of multiple sequence alignments
 
Expasy proteomics tools
Large collection of mainly protein related tools, identification, characterization, pattern searches etc.
 
HelicalWheel
Java applet for helical wheel analysis
 
Helix-Turn-Helix Prediction
predicts helix-turn-helix motifs from a given protein sequence
 
Kyte-Doolittle Hydropathy Plots
composition anaylsis and secondary structure prediction
 
 
PDB protein database
just THE online resource for protein structure (pdb) files
 
PsiPred :: Secondary Structure Prediction
PhD :: Secondary Structure Prediction
PROF :: Secondary Structure Prediction
different secondary structure prediction servers
 
SPORulate
Meta Server for protein structure prediction
 
3D-JIGSAW
Protein homology modelling server
 

SWISS-MODEL: Webserver for comparative modelling

Swiss Pdb Viewer - DeepView: pdb viewer and compartive modelling tool, also calculates H-bonds etc.

VegaZZ Pdb-Viewer: pdb viewer: easy addition of solvent clusters for molecular dynamic simulations, also calculates surface maps eg. elctrostatic potential

Yasara - View:  yet another nice pdb viewer

MOLOC: Molecular Design Software suite: Energy Minimization, Pharmacophore modelling, molecular dynamics

WHAT IF: Web Interface to the famous WHAT-IF suite, all kind of analyzes, check and repair models,                 mutant prediction etc.

Dundee PRODRG2 Server: convert ligand and protein structure-files e.g. for docking in AutoDOCK etc...

MEDock: Maximum Entropy docking of small lignads to proteins

ClusPro :: Docking
Server for protein-protein docking based on electrostatics 
 
PatchDock:: shape complementarity docking
Server for protein-ligand and protein-proteindocking based on shape complementarity
 
UCLA-DOE Server for Structure Anylysis and Validation
3D structure validation using PROCHECK, WHAT_CHECK, SF_CHECK etc...

PDB2MultiGif
generation of rotating animated gifs from pdb files

MovieMaker: generate rotating gif-images from pdb-files and other animations like ligand docking etc.

HAFTUNGSAUSSCHLUSS - LEGAL DISCLAIMER
 


Institute for Molecular Enzyme technology (IMET)                         Heinrich Heine Universität
HHU Duesseldorf at the Research Centre Juelich                          Duesseldorf

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