After about six months or so of having given up on automated docking I have returned with a new biological problem to explore.
I have recently solved the structure of a protein "that shall remain nameless" because I think I have identified a new pocket that no one has targeted before. After asking advice from the ccp4 bulletin board someone suggested using the Uppsalla Software Factories program "Voidoo" for better defining my cavity (http://xray.bmc.uu.se/usf/). As I am quite familiar with USF programs (although have never used Voidoo before) I was quickly able to make a map of all the cavities in my protein using a 1A probe, that I was then able to view in Coot. This gave me an excellent idea of the extent of the pocket along with some ideas of molecules that might fit it.
Before getting out all my Autodock and FlexX scripts again for compound screening I thought I would try out a webservice called "DOCK blaster" based on the docking program DOCK and the ZINC database. It was ridicuously simple to read in my pdb file (with waters and other ligands removed) and equally simple to define the protein site to be docked by simply placing a "fake" phosphate residue into my newly identified cavity and then giving DOCK blaster these coordinates. In a couple of hours I was able to screen three or four sub-sections of the ZINC database and get back fifty or so potential small molecules which, on inspection, seem to fit the site quite well.
I am really impressed with DOCK blaster as it managed to achieve in ten minutes something that took me hours to do last year. Although I have yet to validate the results, it has given me a start. I think the next thing will be to take these fragments and see what Autodock, FlexX and Gold make of them.
Friday 8 January 2010
Thursday 23 April 2009
Docking despair
I work on a number of drug design projects where the number of compounds being produced by the chemists is far greater than I could possibly hope to co-crystallise with the protein and solve the subsequent structures. My hope was that I could use a docking program to quickly get an idea of how compounds might bind which could perhaps help me decide which compounds are interesting enough to put into crystal screens. I have three completely separate projects, and libraries of compounds for all three projects where I know both the experimental binding affinity and structure. Thus I figured the best thing to do was to run these libraries through a number of docking programs and see which predicted my binding conformations best. I have no hope of predicting affinity data because docking algorithms are not up to this yet, but a hint at the order of affinities would be an extra bonus. If this all worked successfully I would then try looking at libraries such as ZINC to try and find totally new compounds.
After about a year, and a couple expensive software licenses, I have come to the conclusion that no current docking programs will be able to help me at this point in time. I have evaluated GOLD, FlexX and Autodock 4 with libraries from all three projects, played around with lots of parameters, and it seems none of these programs can accurately predict binding orientations, and certainly cannot rank compounds in any experimentally meaningful way. Meanwhile the couple ZINC sub-libraries I did look at with both Autodock and FlexX did not manage to dock many compounds in a meaningful way.
I think the reason for this failure is down to the protein structures themselves. Looking at the literature and at the situations where docking has worked well for people, it seems that proteins with very well defined binding sites and obvious hydrogen bond donors/acceptors work well with docking prgrams. Although two of my proteins contain strongly charged positive ions, the rest of the binding pockets rely on hydrophobic interactions which seem to be difficult to model (and hence recognise) by the docking programs. Meanwhile my third protein is a promiscuous aromatic binder whose binding site is necessarily quite unspecific, something that again is probably not good for the success of the docking programs. Thus I think at the moment the docking programs are not yet able to model my systems, and cannot really help with quickly screening my compounds.
However I do have some ideas for using the programs to simulate molecular dynamics...
After about a year, and a couple expensive software licenses, I have come to the conclusion that no current docking programs will be able to help me at this point in time. I have evaluated GOLD, FlexX and Autodock 4 with libraries from all three projects, played around with lots of parameters, and it seems none of these programs can accurately predict binding orientations, and certainly cannot rank compounds in any experimentally meaningful way. Meanwhile the couple ZINC sub-libraries I did look at with both Autodock and FlexX did not manage to dock many compounds in a meaningful way.
I think the reason for this failure is down to the protein structures themselves. Looking at the literature and at the situations where docking has worked well for people, it seems that proteins with very well defined binding sites and obvious hydrogen bond donors/acceptors work well with docking prgrams. Although two of my proteins contain strongly charged positive ions, the rest of the binding pockets rely on hydrophobic interactions which seem to be difficult to model (and hence recognise) by the docking programs. Meanwhile my third protein is a promiscuous aromatic binder whose binding site is necessarily quite unspecific, something that again is probably not good for the success of the docking programs. Thus I think at the moment the docking programs are not yet able to model my systems, and cannot really help with quickly screening my compounds.
However I do have some ideas for using the programs to simulate molecular dynamics...
Monday 13 April 2009
Autodock email list
As a structural biologist I am used to the excellent ccp4 email list populated by the best crystallographers in the world. It is sometimes rather intimidating to post a question, however you always know that you will get an excellent answer...
...and then you have the autodock email list... oh dear...
Although there are one or two people who seem to be genuine scientists, the rest of the posts seem to be written by clueless students just looking to take short-cuts on their projects. I presume that because autodock is free software various teachers around the globe have set assignments using it, however the result seems to be an inundation with stupid questions written in text speak. This is a real shame because molecular docking is a potentially exciting technology which could well benefit from the type of discussions held on the ccp4 email list. I suppose I should just give up on the list, however every now and again something interesting gets written. Perhaps the guys at scripps should think about moderating the list in order to improve the quality?
...and then you have the autodock email list... oh dear...
Although there are one or two people who seem to be genuine scientists, the rest of the posts seem to be written by clueless students just looking to take short-cuts on their projects. I presume that because autodock is free software various teachers around the globe have set assignments using it, however the result seems to be an inundation with stupid questions written in text speak. This is a real shame because molecular docking is a potentially exciting technology which could well benefit from the type of discussions held on the ccp4 email list. I suppose I should just give up on the list, however every now and again something interesting gets written. Perhaps the guys at scripps should think about moderating the list in order to improve the quality?
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