From owner-chemistry@ccl.net Tue Oct 1 08:41:01 2024 From: "Andrea Mauri andrea.mauri/./alvascience.com" To: CCL Subject: CCL: Alvascience releases alvaDesc 3.0 Message-Id: <-55225-241001043833-4291-GXjdwRQ7yhiNTsBmrTqAig|,|server.ccl.net> X-Original-From: "Andrea Mauri" Date: Tue, 1 Oct 2024 04:38:31 -0400 Sent to CCL by: "Andrea Mauri" [andrea.mauri^-^alvascience.com] We are happy to announce that version 3.0.0 of alvaDesc is now available. Alvascience tool, alvaDesc, is a tool designed for the seamless calculation of a wide range of molecular descriptors, molecular fingerprints, and user-defined structural patterns =============================================================== Here are the highlights of alvaDesc v3.0.0: - 133 new molecular descriptors: - Constitutional indices (6) - Ring descriptors (3) - Topological indices (11) - 2D autocorrelations (12) - Geometrical descriptors (1) - RDF descriptors (30) - 3D-MoRSE descriptors (32) - Molecular properties (7) - SASA descriptors (31) - Structural patterns calculation with SMARTS syntax - 3D coordinates calculation - Faster fingerprint ECFPV3 - Principal Component and tSNE analysis on fingerprints - Color and size of plot items using both discrete and categorical values - Filter of molecules using user-defined substructures - Highlight of user-defined substructures and Bemis-Murcko features - Show partial charges for each atom of the molecule - Search in Google Patents/Scholar - Import of SMILES from txt, csv, tsv file formats - Export of descriptors to Excel, SMILES and MDL formats - Menu to open a recent molecular file =============================================================== alvaDesc - KNIME An updated alvaDesc KNIME Plugin is available for compatibility: Pattern node to calculate structural patterns ECFPV3 added to the list of available fingerprints Multithreading support to speed up the calculation =============================================================== alvaDesc - Python An updated alvaDescCLIWrapper (v1.0.10) for Python is available for compatibility: Function calculate_patterns to calculate structural patterns ECFPV3 added to the list of available fingerprints Utility functions get_descriptor_names and get_descriptors_from_blocks =============================================================== alvaModel and alvaRunner New versions of alvaModel (v2.0.10) and alvaRunner (v2.0.10) are also available for compatibility. These versions can handle models making use of structural patterns and ECFPV3. =============================================================== To request a trial version of alvaDesc 3.0 or for additional information, please contact: info/./alvascience.com Additional information can be found at: https://www.alvascience.com/ Linkedin: https://www.linkedin.com/company/alvascience/ YouTube: https://www.youtube.com//./alvascience X: https://x.com/alvascience Facebook: https://www.facebook.com/alvascience/ =============================================================== Andrea Mauri, PhD mail - andrea.mauri/./alvascience.com Alvascience srl - http://www.alvascience.com/ From owner-chemistry@ccl.net Tue Oct 1 11:39:00 2024 From: "Gerard van Westen gerard_+_lacdr.leidenuniv.nl" To: CCL Subject: CCL: 2nd Call for Papers - 13th ICCS Noordwijkerhout - June 1st to 5th 2025 Message-Id: <-55226-241001113728-31600-WRm2YYiWJMwmphgBQh3pkQ(-)server.ccl.net> X-Original-From: "Gerard van Westen" Date: Tue, 1 Oct 2024 11:37:26 -0400 Sent to CCL by: "Gerard van Westen" [gerard-#-lacdr.leidenuniv.nl] C A L L F O R P A P E R S 13th International Conference on Chemical Structures. Abstract submission has opened! The deadline for the submission of abstracts is the 14th of February 2025. NH Leeuwenhorst Conference Hotel, Noordwijkerhout, The Netherlands, 1-5 June 2025 Visit the conference website at https://www.iccs-nl.org, email iccs2025:-:fu- confirm.de, or visit our linkedin group https://lnkd.in/eimzzrRj for more information. Building on past successes of the conference series, the 2025 event will offer a strong scientific program covering all aspects of cheminformatics and molecular modeling. We encourage the submission of papers both on method and algorithmdevelopment as well as applications and case studies. Highest standards of scientific quality and validation of results will be required. For this event the ICCS is seeking presentations of novel research and emerging technologies for the following plenary sessions: Advanced Cheminformatics Techniques Molecular Similarity and Diversity Analysis Chemical Literature and Patent Mining Spectroscopy and Structure Elucidation (Automated) Reaction Handling and Optimization Artificial Intelligence, Machine Learning, and QSAR Consensus, Federated Learning, and Uncertainty Quantification Advances in Large Language Models for Chemistry Synthetic Accessibility and Retrosynthesis Planning Multi-objective and Many-objective Optimization in Drug Design Integrative Structure-Based Drug Design Molecular Dynamics and Free Energy Calculations Structure-based and Rational Drug Design Innovations Modeling Complex Protein Interactions Computer-Assisted Protein Design and Engineering New Modalities and Large Chemical Data Sets Design, Profiling, and Comparison of Compound Collections Advances in DNA Encoded Libraries Covalent inhibitors and PROTACS Biologics and oligonucleotides Open Science, Omics, and Natural Products Open Access Publishing and Collaborative Platforms Findable, Accessible, Interoperable, and Reusable (FAIR) Advances in X-omics Natural Product Drug Discovery We also welcome contributions in other aspects of the computer handling of chemical structure information, such as: automatic structure elucidation combinatorial chemistry and diversity analysis electronic publishing MM or QM/MM simulations modeling of ADME properties material sciences analysis and prediction of structures, grid and cloud computing in cheminformatics > From the submissions the program committee and the scientific advisory board will select around 30 papers for the plenary sessions. All submissions that cannot be included in the plenary sessions will be automatically considered for the poster sessions. We hope to see you in Noordwijkerhout! On behalf of the organizing committee, Gerard van Westen