Hello I am looking into constructing water density maps for protein superfamilies by superimposing all high-resolution structures to detect conserved water positions. Has somebody tried something similar? Are there scripts available that may be adopted or adapted for this purpose? Thank you Shahid Khan -- Dr. Shahid Khan Senior Scientist Molecular Biology Consortium Lawrence Berkeley National Laboratory

Shahid, We did this for Rossmann fold proteins and several other families: https://pubmed.ncbi.nlm.nih.gov/12192068/ https://pubmed.ncbi.nlm.nih.gov/16700049/ Also, see section 4 of https://pubmed.ncbi.nlm.nih.gov/34184009/ for a review of approaches used to identify conserved water molecules in protein structures. Jack -- John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj@missouri.edu<mailto:tannerjj@missouri.edu> https://cafnrfaculty.missouri.edu/tannerlab/ Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A From: Shahid Khan <smkhan@lbl.gov> Date: Thursday, November 25, 2021 at 7:57 PM To: pdb-l@lists.wwpdb.org <pdb-l@lists.wwpdb.org> Subject: pdb-l: Water density maps WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. Hello I am looking into constructing water density maps for protein superfamilies by superimposing all high-resolution structures to detect conserved water positions. Has somebody tried something similar? Are there scripts available that may be adopted or adapted for this purpose? Thank you Shahid Khan -- Dr. Shahid Khan Senior Scientist Molecular Biology Consortium Lawrence Berkeley National Laboratory The archive of messages, sent to pdb-l@lists.wwpdb.org, can be found at: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.wwpdb.org%2Fempathy%2Flist%2Fpdb-l.lists.wwpdb.org&amp;data=04%7C01%7Ctannerjj%40missouri.edu%7C90776e274a274b04f4d308d9b0800739%7Ce3fefdbef7e9401ba51a355e01b05a89%7C0%7C0%7C637734886607410897%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=SbCeznRF769%2F5%2BoWb1jRoXWk3MWKAo3n3daW0GYHWgs%3D&amp;reserved=0 To subscribe or unsubscribe via email, send a message with subject or body 'help' to: pdb-l-request@lists.wwpdb.org

Thanks Jack Shahid On Fri, Nov 26, 2021 at 12:37 PM Tanner, John J. <TannerJJ@missouri.edu> wrote: > Shahid, > > > > We did this for Rossmann fold proteins and several other families: > > > > https://pubmed.ncbi.nlm.nih.gov/12192068/ > > https://pubmed.ncbi.nlm.nih.gov/16700049/ > > > > Also, see section 4 of https://pubmed.ncbi.nlm.nih.gov/34184009/ for a > review of approaches used to identify conserved water molecules in protein > structures. > > > > Jack > > > > > > -- > > John J. Tanner > > Professor of Biochemistry and Chemistry > > Associate Chair of Biochemistry > > Department of Biochemistry > > University of Missouri > 117 Schweitzer Hall > > 503 S College Avenue > Columbia, MO 65211 > Phone: 573-884-1280 > > Email: tannerjj@missouri.edu <tannerjj@missouri.edu> > https://cafnrfaculty.missouri.edu/tannerlab/ > > Lab: Schlundt Annex rooms 3,6,9, 203B, 203C > > Office: Schlundt Annex 203A > > > > > > > > > > *From: *Shahid Khan <smkhan@lbl.gov> > *Date: *Thursday, November 25, 2021 at 7:57 PM > *To: *pdb-l@lists.wwpdb.org <pdb-l@lists.wwpdb.org> > *Subject: *pdb-l: Water density maps > > WARNING: This message has originated from an External Source. This may be > a phishing expedition that can result in unauthorized access to our IT > System. Please use proper judgment and caution when opening attachments, > clicking links, or responding to this email. > > Hello > > I am looking into constructing water density maps for protein superfamilies > by superimposing all high-resolution structures to detect conserved water > positions. > > Has somebody tried something similar? Are there scripts available that may > be adopted or adapted for this purpose? Thank you > > Shahid Khan > > -- > Dr. Shahid Khan > Senior Scientist > Molecular Biology Consortium > Lawrence Berkeley National Laboratory > The archive of messages, sent to pdb-l@lists.wwpdb.org, can be found at: > > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.wwpdb.org%2Fempathy%2Flist%2Fpdb-l.lists.wwpdb.org&amp;data=04%7C01%7Ctannerjj%40missouri.edu%7C90776e274a274b04f4d308d9b0800739%7Ce3fefdbef7e9401ba51a355e01b05a89%7C0%7C0%7C637734886607410897%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=SbCeznRF769%2F5%2BoWb1jRoXWk3MWKAo3n3daW0GYHWgs%3D&amp;reserved=0 > > To subscribe or unsubscribe via email, send a message with subject or > body 'help' to: > pdb-l-request@lists.wwpdb.org > -- Dr. Shahid Khan Senior Scientist Molecular Biology Consortium Lawrence Berkeley National Laboratory