From owner-chemistry@ccl.net Tue Sep 27 00:04:01 2022 From: "Guillaume Brunin guillaume.brunin_._matgenix.com" To: CCL Subject: CCL: Survey on your experience with simulation codes Message-Id: <-54800-220923203302-3450-bs+8ClcQAfJpzVS7Pz0OeA]=[server.ccl.net> X-Original-From: "Guillaume Brunin" Date: Wed, 21 Sep 2022 11:11:12 -0400 Sent to CCL by: "Guillaume Brunin" [guillaume.brunin]![matgenix.com] Dear all, Over the last decades, the field of computational materials science has greatly advanced and is now rich with an impressive diversity and very advanced capabilities. In the jungle of all the possibilities that are out there, it is sometimes difficult to know which would be the better (combination of) tools for our task, what the current and future needs of the community are, and what the general (or specific) feelings are with respect to this situation. With this survey, we hope to be able to paint a more precise picture of the needs of our community and pave the way for the development of new open-source codes/libraries that will fill the existing gaps and be beneficial to all of us. Whether you are a user, a developer, and/or a project manager, we want to hear from you ! The results of this survey will be publicly available- but don't worry, it's all anonymous. If you would like to help us (and, really, help the community), please follow this link to the survey: https://forms.office.com/r/ta3CSj8g3Q Filling this survey will take you about 5 to 15 minutes, depending on how much you have to tell us. Feel free to share this message with your colleagues! We thank you in advance for your time, On behalf of Matgenix, David Waroquiers Guido Petretto Gian-Marco Rignanese Geoffroy Hautier Guillaume Brunin With help from Xavier Gonze Samuel Ponc Matteo Giantomassi From owner-chemistry@ccl.net Tue Sep 27 08:26:00 2022 From: "Andrea Mauri andrea.mauri-,-alvascience.com" To: CCL Subject: CCL: alvaMolecule v2.0.0 Message-Id: <-54801-220927025744-23831-fXiAtCTXmcEsuf3eAk9hyw!A!server.ccl.net> X-Original-From: "Andrea Mauri" Date: Tue, 27 Sep 2022 02:57:41 -0400 Sent to CCL by: "Andrea Mauri" [andrea.mauri:+:alvascience.com] Dear all, We are happy to inform you that we have just released version 2.0.0 of alvaMolecule - our software tool to visualise, analyse, curate and standardize your molecular dataset. We remind you that, alvaMolecule is free for academic and non-commercial use. You can find more information on alvaMolecule at: https://www.alvascience.com/alvamolecule/ Here is the list of the main changes of alvaMolecule: - Import XYZ cartesian coordinates format (*.xyz) - Export dataset as Excel file (*.xlsx) - Delete molecules - Find molecular structures in Google Patents/Scholar - Molecule grid: filter molecules by substructure (SMARTS) - Molecule grid: column value can be set as footer of a molecule cell - Charts: added molecule hint on charts - Charts: added context menu to save data of charts - Charts: added 'Lasso selection' - Highlight substructures (SMARTS) - Highlight Bemis-Murcko features - Standardizers: standardize nitro group as [N+]([O-](=O) - Standardizers: remove radicals preserving usual valence - Standardizers: neutralize atoms - Standardizers: neutralize molecule - Standardizers: custom standardizer with SMIRKS - Checkers: modified the non-standard atom set which now includes the following atoms: H, B, C, N, O, P, S, F, Cl, Br, I - Duplicate analysis: identify duplicated structures - Duplicate analysis: automatically delete duplicated structures - Duplicate analysis: identify molecules with the same value for a specific column - Scaffold analysis: identify the Bemis-Murcko scaffolds If you want to know more about Alvascience solutions, check out our Youtube channel (https://www.youtube.com/channel/UCoiZMgz4L0XT9W_YIpLb2xg) and consider attending one of the following upcoming events: - Clustering and Classification Workshop - NIEHS (online) - October 3-4, 2022- https://www.niehs.nih.gov/news/events/nams2022/index.cfm - SCI-RSC Workshop on Computational Tools for Drug Discovery - SOCI (Birmingham) - November 23, 2022 - https://www.soci.org/events/fine- chemicals-group/2022/scirsc-workshop-on-computational-tools-for-drug- discovery-2022 Also, you can watch the recording of the latest event (ACS Fall - Chicago): De novo molecular design with genetic algorithms using alvaBuilder - https://www.morressier.com/o/event/62daeef3a6fd3a00196fa00a/article/630fcb5b7 e215f5e7f375705 Best regards, Andrea Mauri