So, Thomas, you don't see anything wrong in the way I compute the surfaces? The numbers should be like that, right?
The reason I need both the molecular surface and the SASA in not directly related to a physical quantity. I do SQM scoring of compounds bound to proteins, but the bulkier molecules, which are usually non-binders, tend to yield lower interaction free energies. Thus, I thought to try these two surface types of both the protein and the ligand as descriptors in a machine learning-based attempt to balance these differences and improve the scoring. It remains to be seen in practice which of these two types (molecular surface or SASA) are more useful for my purpose. I also use other molecular descriptors, but I don't want to elaborate on this because it's out of topic. Best, Thomas On Thu, 21 May 2020 at 21:57, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > Hi Thomas and Blaine, > > SASA is probably the correct feature to evaluate here, not molecular > surface. Of course it may depend the actual goal of this exercise, but > typically when talking about interface surface, you're putting that into > context with binding energy or solvation effects, and only SASA is > meaningful for that as far as I know. > > The difference between SASA and molecular surface is a matter of size and > shape. For a very uneven shape (lots of small pockets or protuberances), > going from molecular surface to SASA will flatten the surface, which can > result in a smaller area, even though the volume is increased. > > You may be interested to check out PISA for this task, it's the tool the > PDB uses to determine biological assemblies: > https://www.ebi.ac.uk/pdbe/pisa/ > > PyMOL's and PISA's results should be similar, but PyMOL is probably easier > to handle :-) > > Cheers, > Thomas > > > > On May 21, 2020, at 4:37 AM, Mooers, Blaine H.M. (HSC) < > blaine-moo...@ouhsc.edu> wrote: > > > > Hi Thomas, > > > > If you display the SASA of the protein in PyMOL's viewport, > > you will see that it and that of the ligand have huge overlaps > > How do you define the interface in such a situation and how > > do you interpret it? > > > > The interface of the molecular surfaces seems easier to interpret. > > > > Best regards, > > > > Blaine > > > > Blaine Mooers, Ph.D. > > Associate Professor > > Department of Biochemistry and Molecular Biology > > College of Medicine > > University of Oklahoma Health Sciences Center > > S.L. Young Biomedical Research Center (BRC) Rm. 466 > > 975 NE 10th Street, BRC 466 > > Oklahoma City, OK 73104-5419 > > > > ________________________________________ > > From: Thomas Evangelidis [teva...@gmail.com] > > Sent: Wednesday, May 20, 2020 9:14 AM > > To: pymol mailinglist > > Subject: [EXTERNAL] [PyMOL] How to compute the interface surface between > ligand and protein? > > > > Greetings, > > > > I want to compute the interface surface between the ligand and the > protein in batch mode for hundreds of thousands of PDBs, like the attached > one (sample.pdb). I am interested in the interface surface of both of them. > First I create two new molecules, the protein, and the ligand, and I work > with them because the results I get when working with the original molecule > (which contains both protein and ligand) are different. > > > > load sample.pdb > > create protein, polymer > > create ligand, resn LIG > > delete sample > > > > select prot_interface, protein within 3.5 of ligand; > > set dot_solvent, 0; > > get_area prot_interface; > > set dot_solvent, 1; > > get_area prot_interface; > > > > select lig_interface, ligand within 3.5 of protein; > > set dot_solvent, 0; > > get_area lig_interface; > > set dot_solvent, 1; > > get_area lig_interface; > > > > protein interface molecular surface = 1216.239 Angstroms^2 > > protein interface SASA = 763.095 Angstroms^2 > > ligand interface molecular surface = 748.867 Angstroms^2 > > ligand interface SASA = 977.608 Angstroms^2 > > > > I still don't understand why the interface molecular surface of the > ligand is smaller than the interface SASA, while the opposite happens with > the protein. Could someone please explain this to me and verify that I am > computing the interface surfaces correctly? > > > > I thank you in advance. > > Thomas > > > > > > > > -- > > > > ====================================================================== > > > > Dr. Thomas Evangelidis > > > > Research Scientist > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: teva...@gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/
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