Yes correct, the numbers should be like that. I don't see anything wrong with your approach.
Thanks for the background info. Maybe you can give us an update once the study is over, sounds interesting! Cheers, Thomas > On May 22, 2020, at 12:41 AM, Thomas Evangelidis <teva...@gmail.com> wrote: > > 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, Prague, Czech Republic > & > CEITEC - Central European Institute of Technology, Brno, Czech Republic > > email: teva...@gmail.com, Twitter: tevangelidis, LinkedIn: Thomas Evangelidis > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
