Resources and links

On this page you will find some references to databases, software tools, and web services that we find either useful, interesting, or just good to know.

Helpful web sources:

... related to Proteins:

  • Robetta: Full-chain Protein Structure Prediction at Baker Lab at the University of Washington.
  • PredictProtein: Structure Prediction and Sequence Analysis
  • The Zinc-Finger Consortium: Software for designing zinc-finger arrays.
  • SCOP: Structural Classification of Proteins.
  • ProteinCalculator: Compute various parameters such as absorbance, weight, charge etc for a given amino acid sequence.

... related to DNA:

  • caDNAno: Computer-aided design of DNA origami structures.
  • CanDo: Computer-aided engineering for DNA origami.
  • IDT Scitools: Oligonucleotide design and analysis tools (incl. mfold hairpin prediction).
  • NUPACK - nucleic acid package: Thermodynamic DNA analysis and sequence design.
  • Prediction of intrinsic DNA curvature based on sequence.
  • Generates a 3d model (pdb-format) of a DNA molecule based on sequence.
  • Computes various physiochemical parameters for a given DNA sequence.
  • BioMath: Quickly convert DNA grams to moles etc.
  • EnzymeX: DNA restriction digest analysis and DNA-to-protein translation services.
  • DNA from the Beginning: A primer on the basics of DNA, genes, and heredity.

... related to visualizing Proteins and DNA:

The Protein Data Bank hosts the current body of structural data on proteins and their complexes that has been acquired so far by researchers from all over the world. Beyond that, under 'General Education' it also offers the 'Molecule of the Month': concise but at the same time thrilling accounts on selected molecules to be found in the Protein Data Bank. The stories are presented by David S. Goodsell, together with beautifully painted images of the protein structures. 


To the right you can see a reproduction of Goodsell's painting of the Cholera Toxin. Such pore-proteins have inspired some of our research on DNA origami nanopores. If you ever wondered why some bacteria make you sick, read this shocking story about Cholera (original story and how it relates to other bacterial toxins to be found here):


Cholera Toxin

Sept 2005 Molecule of the Month by David S. Goodsell 


"Bacteria pull no punches when they fight to protect themselves. Some bacteria build toxins so powerful that a single molecule can kill an entire cell. This is far more effective than chemical poisons like cyanide or arsenic. Chemical poisons attack important molecules one by one, so many, many molecules of cyanide are needed to kill a cell. Bacterial toxins use two strategies to make their toxins far more deadly than this. The first strategy used to build super-deadly toxins is to use a targeting mechanism to deliver the toxin directly to the unlucky cell. Cholera toxin, shown here from PDB entry 1xtc, has a ring of five identical protein chains, colored blue here, which binds to carbohydrates on the surface of cells. This delivers the toxic part of the molecule, colored red, to the cell, where it can wreak its havoc. 


The second deadly strategy is to use a toxic enzyme instead of a chemical poison. Enzymes are designed to perform their reactions over and over again, hopping from target to target and making their chemical changes. Thus, one enzyme can modify a whole cell full of molecules. Cholera uses this strategy once it gets inside cells. The toxic portion hops from molecule to molecule, disabling each one in turn, until the entire cell is killed.


The catalytic portion of cholera toxin performs a single function: it seeks out the G proteins used for cellular signaling and attaches an ADP molecule to them (for more on G-proteins, see the Molecule of the Month for March 2004 ). This converts the G-protein into a permanently active state, so it sends a never-ending signal. This confuses the cell, and among other things, it begins to transport lots of water and sodium outwards. This floods the intestine, leading to life-threatening dehydration." is a really fun computer game of high scientific and educational value! Your task as a player is to find solutions to real protein folding puzzles. By manipulating the arrangement of backbone and restgroups of a starting protein structure one seeks to find structures that score higher, i.e. that have lower energies. Playing has benefits to science and to yourself! For science: While you might not only contribute to solve an unknown protein structure, the makers of the game also monitor how humans solve these puzzles, with the goal to find better strategies for computational protein structure prediction. For yourself: While playing, you will not only obtain a valuable feeling for the diverse properties and shapes of the amino acids that make up proteins, but you will also get an idea why computational protein structure prediction is a really difficult task. Quite frequently you will end up in a local energy minimum structure and then you have to ask yourself: how can I get to an even lower energy structure? was conceived in the Baker Lab at the University of Washington and the lead game creator is Adrien Treuille.