Querying 1TB on a MacBook Pro with Python dataframes
Macs in Chemistry Blog
by chris
2d ago
This looks interesting, handling large datasets is becoming more common and I’m always on the lookout for useful tools because pandas requires your dataframe to fit in memory.  …. my rule of thumb for pandas is that you should have 5 to 10 times as much RAM as the size of your dataset. So if you have a 10 GB dataset, you should really have about 64, preferably 128 GB of RAM if you want to avoid memory management problems.  Using Ibis a portable data frame library vast datasets can be explored (>1 billion rows). There is an introduction here https://ibis-project.org/posts/1t ..read more
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Clipboard-to-SMILES-Converter
Macs in Chemistry Blog
by chris
2w ago
I first mentioned this utility back in March and I’ve been using it since then and I have to say I find it invaluable. Clipboard-to-SMILES-Converter is a lightweight macOS app designed to simplify the conversion process between a variety of chemical notations for chemical structures, such as Images of Molecules, SMILES, SELFIES, RdKit Mols, InChI, CAS numbers, and IUPAC directly in the clipboard. https://github.com/O-Schilter/Clipboard-to-SMILES-Converter Well worth giving it a try ..read more
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ChEMBL 15 Year Symposium 
Macs in Chemistry Blog
by chris
2w ago
I’m sure many people have used ChEMBL at some point or other and it is great to see a 15 year celebration. it is also the 10th anniversary of SureChEMBL. ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. Date : 1 – 2 October 2024Timezone: Europe/LondonVenue: EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1RQ. UKDay 1 Workshops IN PERSON ONLY | EMBL-EBI Main Building, Garden & Courtyard roomsDay ..read more
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Latest Cache Challenge
Macs in Chemistry Blog
by chris
3w ago
The latest (6th) Cache challenge has been released. The target is SETDB1 Participants are asked to find molecules occupying one or multiple subcavities of the histone binding groove of the SETDB1 triple Tudor domain (TTD). https://cache-challenge.org/challenges/finding-ligands-targeting-the-triple-tudor-domain-of-setdb1 The structure above was displayed using the brilliant 3Dmol.js (https://3dmol.csb.pitt.edu) Only a few days left Application closes 2024-06-22 ..read more
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ChimeraX updated
Macs in Chemistry Blog
by chris
1M ago
UCSF ChimeraX version 1.8 has been released, and can be downloaded here. https://www.rbvi.ucsf.edu/chimerax/download.html This update includes – show worm depictions of attribute values (B-factor, conservation, etc.)  using Render by Attribute tool or “cartoon byattribute” command – show attribute values with atomic radii using Render by Attribute or  “size byattribute” – Select by Attribute graphical interface – Join Models generalized to any covalent bond (not just peptide) – show multiple alternate locations simultaneously with “altlocs show” – “pbond” command to create arbitrary ..read more
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MolX viewer
Macs in Chemistry Blog
by chris
1M ago
Another molecule viewer, MolX viewer from Genophore is an intuitive biomolecule and small molecule viewer. https://genophore.com/app/protein_structures/standalone_molx/ The standalone viewer is pretty fully featured, but there is an option to create an account to unlock extra features. There is also the ability to browse known drugs with associated data ..read more
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Apple Intelligence an approach to AI privacy?
Macs in Chemistry Blog
by chris
1M ago
This weeks WWDC gave details of upgrades to the various operating systems. Great to see the calculator make it to the iPad at last, the Math notes feature looks super cool, being able to write equations using the Apple Pencil and have them solved real time is great, very nice that you change variable on the fly and even create graphs (I think Math Notes will also be available on the Mac?). Perhaps more interestingly they also gave details of the Apple approach to AI/ML (I’m not sure why they had to coin Apple Intelligence). Whilst it is clear that the neural processing unit on the new M-serie ..read more
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Molsoft ICM-Pro update and new products
Macs in Chemistry Blog
by chris
1M ago
The ICM-Pro + VLS software has undergone significant updates and improvements in its built-in functionalities for modeling, docking, GUI, and visualization. These enhancements include pre-built models in MolScreen for quickly predicting the target properties and activities of compounds. Notable new features encompass advanced MD functionalities, new AI models and AI layers for property and target prediction, extended cheminformatics functions, an improved 3D ligand editor, and direct access to AlphaFold models, as reviewed below. Additionally, new modules have been developed for specialized GP ..read more
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Sort & Slice: A Simple and Superior Alternative to Hash-Based Folding for Extended-Connectivity Fingerprints
Macs in Chemistry Blog
by chris
1M ago
An interesting alternative to hash-based folding on arXiv. https://arxiv.org/abs/2403.17954 Code is on GitHub https://github.com/MarkusFerdinandDablander/ECFP-substructure-pooling-Sort-and-Slice ..read more
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Sire paper out.
Macs in Chemistry Blog
by chris
1M ago
Sire is a Python/C++ library that is used both to prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of many other programs and libraries. The full paper is here. https://doi.org/10.1063/5.0200458 There are builds for three versions of Python (currently 3.10, 3.11, and 3.12) for Windows, MacOS, and Linux. Packages are built using GitHub Actions, with compilation taking between 90 and ..read more
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