Re: [ccp4bb] AI papers in experimental macromolecular structure determination

Hi Andrea, Here is something interesting on the extraction of information on protein dynamics from cryo-EM data: https://doi.org/10.1038/s42256-020-00290-y Best, Tushar. On Tue, 3 Aug 2021 at 19:48, Shekhar Mande wrote: > In particle picking, you may wish to include the following: > >

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

Thanks Andrea for this! One more for crystallization: Ng JT., Dekker C., Kroemer M., Osborne M., von Delft F., (2014), Acta D, 70, 2702 - 2718 On 03/08/2021 12:43, Thorn, Dr. Andrea wrote: Dear colleagues, I have compiled a list of papers that cover the application of AI/machine

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

In particle picking, you may wish to include the following: George, B., Assaiya, A., Roy, R.J. *et al.* CASSPER is a semantic segmentation-based particle picking algorithm for single-particle cryo-electron microscopy. *Commun Biol* 4, 200 (2021). https://doi.org/10.1038/s42003-021-01721-1 On

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

For model validation, this paper used machine learning (Random Forest) to detect peptide problems: https://doi.org/10.1107/S1399004715008263 Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Bernhard > Rupp > Sent: Tuesday, August 3, 2021 22:00 > To:

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

Maybe we should get to the root of this - what qualifies as machine learning and what not? Do nonparametric predictors such as KDE qualify? https://www.ruppweb.org/mattprob/default.html Happy toa dd to the confusion. -Original Message- From: CCP4 bulletin board On Behalf Of Tim

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

One more: BraggNet: integrating Bragg peaks using neural networks B. Sullivan, R. Archibald, J. Azadmanesh, V. G. Vandavasi, P. S. Langan, L. Coates, V. Lynch and P. Langan J. Appl. Cryst. (2019). 52, 854-863 Pavel On Tue, Aug 3, 2021 at 4:53 AM Thorn, Dr. Andrea < andrea.th...@uni-hamburg.de>

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

Hello Andrea, profile fitting, like it is done in mosflm (https://doi.org/10.1107/S090744499900846X) or evalccd, or ... probably also qualify as AI/machine learning. Best wishes, Tim On Tue, 3 Aug 2021 11:43:06 + "Thorn, Dr. Andrea" wrote: > Dear colleagues, > I have compiled a list of

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

Andrea, you may want to include this one: Using support vector machines to improve elemental ion identification in macromolecular crystal structures. Morshed N, Echols N, Adams PD Acta Cryst. D71, 1147-58 (2015). Pavel On Tue, Aug 3, 2021 at 4:53 AM Thorn, Dr. Andrea <

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

Hello, In the particle picking section, you may want to include these two: Wagner T, Merino F, Stabrin M, Moriya T, Antoni C, Apelbaum A, Hagel P, Sitsel O, Raisch T, Prumbaum D, et al (2019) SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Communications

[ccp4bb] Postdoctoral Fellowship at Pfizer

Dear all, We are seeking an enthusiastic and driven postdoctoral fellow to join the Structural and Molecular Sciences (SMS) Department at the Pfizer campus in Groton, Connecticut. This fellowship offers the unique opportunity to learn about the drug and vaccine development process in the

[ccp4bb] AI papers in experimental macromolecular structure determination

Dear colleagues, I have compiled a list of papers that cover the application of AI/machine learning methods in single-crystal structure determination (mostly macromolecular crystallography) and single-particle Cryo-EM. The draft list is attached below. If I missed any papers, please let me

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2021

Dear all, the next MX-proposal application deadline: September 01, 2021 is approaching NEW: REMOTE OPERATION IS NOW POSSIBLE AT BLs14.1 AND 14.2. PARTICPATION IN REMOTE TRAINING COURSE IS REQUIRED. As usual, all proposals will be handled by our electronic user portal GATE,

[ccp4bb] Extended PDB IDs and PDB DOIs now available in PDBx/mmCIF files

Dear CCP4BB, wwPDB, in collaboration with the PDBx/mmCIF Working Group , has set plans to extend the length of ID codes for PDB and Chemical Component Dictionary (CCD) ID entries in the future. These extended formats are