Preeti Choudhary
142 posts
@preeti_cy
Decipher nature's hidden codes by profession. Senior Bioinformatics Scientist at PDBe, EMBL-EBI🖖🤓
📰 Just published! 🔍 Explore how to use PDBe tools for small molecule analysis in the Protein Data Bank 🧪 🌐 Learn about resources like PDBe-KB Ligand Pages & more! 📖 Read in #ProteinScience: doi.org/10.1002/pro.70… @ProteinSociety #DrugDesign #StructuralBiology #STEM
🚨 New from PDBe! Check out the revamped PDBeChem service with enhanced Ligand Pages! 🔍 Explore detailed ligand data, interaction stats, bound structures, related ligands, and more—all in one place. 👉 Read more in the news: ebi.ac.uk/pdbe/news/pdbe…
Announcing new open-source Python package: aisuite! This makes it easy for developers to use large language models from multiple providers. When building applications I found it a hassle to integrate with multiple providers. Aisuite lets you pick a "provider:model" just by changing one string, like openai:gpt-4o, anthropic:claude-3-5-sonnet-20241022, ollama:llama3.1:8b, etc. pip install aisuite Open-source code with instructions: github.com/andrewyng/aisu… Thanks to Rohit Prsad, Kevin Solorio, @standsleeping, Jeff Tang and @Johnsanterre for helping build this!
PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank 1. PDBe has developed new tools to facilitate the analysis of small molecules in the PDB, enhancing data accessibility and insight into ligand-macromolecule interactions. The tools—PDBe CCDUtils, PDBe Arpeggio, and PDBe RelLig—enable researchers to explore ligand data with greater depth and accuracy. 2. PDBe CCDUtils provides enriched ligand data by parsing and processing molecular structures, supporting researchers in standardizing ligand identification across PDB entries. This tool also generates high-quality 2D and 3D visualizations of ligands, enabling a comprehensive view of small molecules. 3. PDBe Arpeggio analyzes detailed interactions between ligands and macromolecules, identifying specific contact points such as hydrogen bonds and hydrophobic interactions, which are crucial for understanding ligand binding. 4. PDBe RelLig classifies ligands based on their functional roles (e.g., cofactor-like, reactant-like, or drug-like), helping researchers distinguish biologically relevant molecules from experimental artefacts, thereby supporting accurate interpretation of biological functions. 5. These tools, along with PDBe-KB’s ligand pages, provide an integrated view of ligands in their biological context, making it easier to visualize interactions, assess binding sites, and explore molecular properties in drug discovery and structural biology research. @preeti_cy @PDBeurope 💻Code: • PDBe CCDUtils: github.com/PDBeurope/ccdu… • PDBe Arpeggio: github.com/PDBeurope/arpe… • PDBe RelLig: github.com/PDBeurope/rell… 📜Paper: biorxiv.org/content/10.110… #Bioinformatics #PDB #DrugDiscovery #StructuralBiology #LigandAnalysis
RIP Google Search ? OpenAI just launched ChatGPT Search and it's INSANE Here are 7 new Features of ChatGPT you don't want to miss:
❗️Just under 2 weeks left until our webinar on available resources to help with starting model selection for #moleculardynamics simulations 🗓️10 September 2024 at 15:00 CEST ➡️registration: bit.ly/3M5LcNR @PDBEurope
The paper on the recently announced NextGen Archive has been published!! The PDB NextGen archive provides sequence annotation from external resources such as UniProt & Pfam to add to the content provided in the structure model files. ⬇️ Read more ⬇️ doi.org/10.1093/databa…
This box will test people's bravery🤣🤣Gets them every time! 👉 cepeio.com/spider-e01
PDBe & ligand-focused: 'Accessing Enhanced Small Molecule Information in the Protein Data Bank in Europe' by @preeti_cy ⬇️ Read here⬇️ rsccicag.org/index_htm_file…
@PDBeurope @pnas Don't forget to mention the 466 sars-cov-2 mpro inhibitor complexes deposited by @Darenfearon on behalf of the @covid_moonshot project spearheaded by the @XChem_DLS @DiamondLightSou team! phew!!
On #WorldVeganDay, we’re celebrating soybeans! Our featured article explores the secret behind their distinctive "beany" flavour. The protein behind this process inspired this wonderful #PDBart by Thanatpohn Siriwatdeachakul from @SPFvisualart 🔗ebi.ac.uk/pdbe/news/unlo…
We’re honoured to receive the German AI Prize 2023! From #AlphaFold to #Imaging, have a look at some of the ways in which we use and develop AI tools in the life sciences: embl.org/news/science/e… #ArtificialIntelligence #KIPreis2023
