Hi Mark, Have you ever looked at Optipharm for shape comparison?
https://www.nature.com/articles/s41598-018-37908-6 <https://www.nature.com/articles/s41598-018-37908-6> Or Shape-it http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/shape-it/1.0.1/shape-it.html Cheers Chris > On 4 Nov 2020, at 14:28, rdkit-discuss-requ...@lists.sourceforge.net wrote: > > From: Mark Mackey <m...@cresset-group.com <mailto:m...@cresset-group.com>> > To: Lewis Martin <lewis.marti...@gmail.com > <mailto:lewis.marti...@gmail.com>>, RDKit Discuss > <rdkit-discuss@lists.sourceforge.net > <mailto:rdkit-discuss@lists.sourceforge.net>> > Subject: Re: [Rdkit-discuss] GPU Implementation of shape-based 3D > overlap on rdkit? > Message-ID: > > <dbbpr08mb4235128b45e0f546acfc5adb97...@dbbpr08mb4235.eurprd08.prod.outlook.com > > <mailto:dbbpr08mb4235128b45e0f546acfc5adb97...@dbbpr08mb4235.eurprd08.prod.outlook.com>> > > Content-Type: text/plain; charset="utf-8" > > Hi Lewis, > > The standard shape alignment algorithm that everyone uses is from Grant & > Pickup 1996 > (https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291096-987X%2819961115%2917%3A14%3C1653%3A%3AAID-JCC7%3E3.0.CO%3B2-K > > <https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291096-987X%2819961115%2917%3A14%3C1653%3A%3AAID-JCC7%3E3.0.CO%3B2-K>). > > It?s a Taylor-series-like expansion using spherical Gaussians as stand-ins > for hard spheres - you take the atomic volumes, subtract off the pairwise > overlaps, add back in the three-way overlaps, subtract off the four-way > overlaps, and so on. I did a fair few tests some years back and you really > need to go to 6 terms to get decent accuracy. However, all of the commercial > algorithms (ROCS, Phase Shape, etc) seem to truncate at 2, so go figure. OTOH > the ?high throughput? versions all seem to be operated with ludicrously low > number of conformations so the error in incomplete coverage of conformer > space dwarfs the 5% noise that you get from truncating at 2 terms rather than > 6. > > If you want something slightly more accurate at the same computational cost, > look at WEGA (https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.23603 > <https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.23603> and references > therein) which heuristically corrects for some flaws in the truncated > Grant&Pickup calculations. > > If you want a fast GPU-accelerated version, then forget about actually > applying the algorithm directly[*]. Instead, to compare a reference molecule > A to a database molecule B, precompute a grid over A containing the pairwise > overlap value of an atom at each point in the grid with A. You can then > compute the shape overlap for a given orientation of B by a simple 3D texture > lookup rather than faffing around trying to compute exponential functions.. > This is simplified by assuming that all atoms have the same atomic radius and > neglecting hydrogens (we?re going for speed over accuracy here, remember?) > You can get a similar lookup texture for gradients, I think. One thing GPUs > are really good at is texture lookups and interpolation. They?re less good at > evaluating exponential functions. Your GPU algorithm is then a massively > parallel CG or NR optimiser with the objective function computing shape > overlap values for as many molecules as you can cram into GPU memory all in > parallel. > > [*] gWEGA (I believe) is a GPU-accelerated version of the standard WEGA > algorithm and based on the published timings is an order of magnitude or more > slower than fastROCS > > Having said all of that, our GPU-accelerated shape similarity function just > brute forces through the overlap series to sixth order, as (a) my happy place > is on the accuracy side of the speed/accuracy tradeoff, and (b) our > electrostatic similarity calculations are sufficiently complex that making > the shape function faster wouldn?t be that much of a net win. As a result, > take all of the above with a grain of salt ?. > > Regards, > Mark > > -- > Mark Mackey > Chief Scientific Officer > Cresset > New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, > UK > tel: +44 (0)1223 858890 mobile: +44 (0)7595 099165 fax: +44 (0)1223 > 853667 > email: m...@cresset-group.com > <mailto:m...@cresset-group.com><mailto:m...@cresset-group.com > <mailto:m...@cresset-group.com>> web: www.cresset-group.com > <http://www.cresset-group.com/><http://www.cresset-group.com/ > <http://www.cresset-group.com/>> skype: mark_cresset
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