Drug design puzzles coming your way!

Hi everyone,

One of the problems that drug designers face seems innocuous at first: what would happen if a single atom in the small molecule changed from a carbon to a nitrogen or vice versa? Will this make the drug bind better to my protein target? At first glance, if you just look at the properties of the elements it might seem like an easy solution. Carbon in small molecules is mostly inert and “hydrophobic” while nitrogen is a “polar” atom and can either accept or donate hydrogen bonds. If a crystal structure is available, drug designers will replace a carbon with a nitrogen to form a hydrogen bond, which should increase activity. However, this can cause a conformational change in the ligand and reduce binding or the chemical properties change in such a way that it is hard to predict.

As you start to embark on your on drug designs for protein targets, you will be faced with a similar challenge. To this end, we have created a dataset of crystal structures with small molecules bound that have a single atom change, a carbon to a nitrogen or a nitrogen to a carbon. As your first drug design puzzle, you will be tasked to determine at which positions to change in order to increase binding to the target. To add on to the excitement, we have given the exact same dataset to our drug designers. At the end of the series of puzzles, we will post the results to see who did better!

Since these will be the initial drug design puzzles, we are looking for a lot of feedback. Functionality is limited in these puzzles (don’t worry, we will give you many more tools in the future and new gameplay modes!) in order to do a thorough testing of the interface. If we can, we will implement the requests that you make.
What is coming in the future?

New tutorials: Follow the steps of a group of scientist as they developed a new small molecule
New gameplay modes: Free design and synthesis based design
New media: chats with scientists and thoughts on the future of drug design

Questions? Add them here and we'll keep them in mind to answer in future posts!

( Posted by  free_radical 83 1754  |  Wed, 07/22/2015 - 15:39  |  2 comments )
2
spmm's picture
User offline. Last seen 10 weeks 18 hours ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
ETA?

Sounds like fun when are they coming?

Joined: 04/24/2014
Groups: None
ETA

Relatively soon (as in within more than likely within the next few weeks, possibly*). :) As always we don't release exact dates, as we want to ensure as best we can that things are working well first.

* could be subject to change if unexpected bugs come up

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons