Useful Websites

Topics

1. Literature and sequence

databases

Literature search

 

 

 

Search a DNA database

 

 

 

Search a protein sequence database

 

 

Bacterial genomes

 

 

Human genomes

 

 

 

Model organisms

 

 

 

 

 

 

 

 

2. Analyse DNA sequence

Predict genes

 

Translate DNA sequence

 

3. Analyse protein sequence

Functional annotation

 

 

Protein identification by ...

 

 

 

4. Compare your protein sequence

to other proteins

Homology search in sequence 

and structure databases

 

Multi-sequence alignment 

and tree visualization

 

 

 

 

 

 

Multi-sequence alignment databases

 

 

Patterns, motifs, domains

 

 

 

 

 

5. Get a 3D model

If an experimental structure is available:

Get the coordinates ...

Get secondary structure information ...

 

 

If only C(alpha) coordinates are

available:

generate backbone and side chain

coordinates

 

Structure modelling

 

 

Quality check of a structure model

 

 

Otherwise: do a secondary structure

prediction

 

 

 

 

6. Visualize a protein structure

Visualize PDB structure

 

 

 

 

Browser plug-ins

 

Visualize ligand interactions

 

Calculate surface and cavities

 

 

 

7. Analyze protein structure

Search for similar structure

 

Assign to a protein architecture

 

 

 

 

 

Enzyme structures

 

Ramachandran plot

 

Side chain interactions

 

Solvent accessibility

 

 

Interactions

 

 

 

8. Analyze protein function

Metabolic databases

 

Active sites in enzymes

 

 

Protein families

 

 

 

 

 

9. Other useful sites

Catalogs of databases

 

 

 

 

 

 

Courses

 

 

 

Bioinformatics links

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Remote server

Medline

ISI Web of Science

Deutsches Patent- und Markenamt

Patent search at US Patent and Trademark Office

 

 

GenBank

EMBL-DB

DDBJ

 

UniProt

Swiss-Prot

PIR

 

Completly sequenced

Sequencing in progress

 

Human genome project

Human SNPs

Human gene mutations

 

EcoCyc (E.coli)

SGD (Yeast)

MIPS (Yeast)

TAIR (A.thaliana)

Acedb (C.elegans)

http://www.acedb.org/

MGI (Mouse)

 

 

 

GeneMark

 

ExPASy

 

 

GeneQuiz

Network Protein Sequence Analysis

 

pI, MW, sequence tag, peptide mass

fingerprinting

 

 

 

BLAST

FASTA

 

Server MultAlin

Match-Box Web Server

Software to be downloaded:

Download ClustalX

Tree-Puzzle: Reconstruction of phylogenetic

trees

TreeView: Visualization of Clustal results

 

 

SYSTERS cluster

Pfam

 

InterPro

Pfam

Prints

ProDom

ProSite

 

 

 

... from PDB

 ... from DSSP

Software to be downloaded:

Download the program DSSP (UNIX)

 

 

MaxSprout

 

 

Swiss-Model

Structure Prediction Meta-Server

 

Model validation

Biotech valiation suite for protein structures

 

GOR

NNPredict

Predator

PredictProtein Server

PSA

 

 

Visualize PDB structure

Software to be downloaded:

RasMol

Kinemage

SwissPdbViewer

 

Software to be downloaded:

Chime

Software to be downloaded:

Ligplot

Software to be downloaded:

Surfnet

naccess

 

 

DALI server

 

SCOP

CATH

CAMPASS

list of SSEs

Protein topology cartoons

 

... by enzyme classification (E.C.)

 

Plotting

 

Atlas of side chain interactions

 

Solvent accessibility

Accessible polar fraction

 

Protein-drug contact

Single residues contact

Protein-protein interaction server

 

 

Biochemical Pathways (Boehringer)

U of M Biodegradation database

 

PROCAT

ENZYME

 

Antibody Resource Page

Esther

Directory of P450-containing systems

Cytochrome P450 Database

Lipase Engineering Database

 

 

Overview of Strain Collections

DBCAT

ExPASy tools

Amos' WWW links page

BioHunt

BioCatalog (index to biological software)

BIOSCI (communication forum)

Antibody database

 

 

Principles of Protein Structure

Structure Prediction Flowchart

 

Bioinformatik.de

http://www.bioinformatik.de/

 

 

 

 

 

 

 

News


Our new homepage is almost finished and this site will not be updated anymore.


In 2016, Uwe Bornscheuer has published News & Views articles in "Nature" and in "Nature Chem. Biol.", a "Perspectives" contribution in the journal "Science" and aresearch article in the journal "Nature Chem."


Johannes Kabisch (junior research group leader) has accepted a position as Junior-Professor at the TU-Darmstadt and Robert Kourist is now full Professor at the TU-Graz, congratulations!


Daniel Last (#51) has finished his PhD!


Uwe Bornscheuer has published his 25th contribution (an Editorial) in the top chemistry journal "Angew. Chem. Int. Ed."


Uwe Bornscheuer has received the "Stephen S. Chang Award" of the Am. Oil. Chem. Soc. (AOCS).


Our paper on the discovery of (R)-selective amine transaminases has been highlighted as "Best Design Concept" by Nat. Chem. Biol.


Author profile:

An author profile about Uwe Bornscheuer has been published in Angew. Chem. Int. Ed.


Contact
Prof. Dr. Uwe Bornscheuer
Institute of Biochemistry
Dept. of Biotechnology & Enzyme Catalysis
Felix-Hausdorff-Str. 4
D-17487 Greifswald/ Germany

Phone:
+49 (0)3834-86-4367
+49 (0)3834-86-4391 (Secr.)
Fax:
+49 (0)3834-86-794367
E-Mail:
uwe.bornscheuer