DOCK Blaster:Broken molecules
You may at first be somewhat alarmed to see a number of broken molecules at the top of a DOCK Blaster hit list.
First, please do not panic.
These are a side effect of a very high throughput approach to molecular docking that makes it possible for us to offer free docking for everyone on our website. Of course they are incorrect, and our long term goal is to eliminate them. However, in our work in the lab, we have become accustomed to seeing a small number of "broken" molecules among the top 50 or so compounds. Our approach is to just skip the molecule and move on to the next one. We suggest you do the same.
The most common functional group associated with broken molecules is sulfones, sometimes part of sulfonamides. Another common motif is ortho- and meta-methoxyphenyl. Molecules appear disconnected, often with oxygens freely floating in space nearby. The problem arises because of a bug. Given over 13 million molecules in ZINC, the most pragmatic approach has been to fix them as we find them.
In addition to broken molecules, there are also molecules that are probably wrong: wrong tautomers, wrong protonated states, wrong conformations.
In all cases, if you find a broken molecule, you can tell us about it in several ways.
1. You can use the "flag" icon next to each molecule to tell us what is wrong.
2. You can write a wiki page to document the problem you see
3. You can write to support at docking.org describing the problem
Thank you for your patience. We hope you agree that as undesirable as broken molecules are, they are a relatively small price to pay for a free service. We also hope to eradicate all of these brokens from our database in a campaign we are calling "the global war on error". (Thanks to G Bricogne for this).