Posts

The Beauty of Proteins

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In this blog, I’ll share some captivating protein visualizations I rendered, along with the fascinating stories behind them. All these visualizations were created using ChimeraX , a powerful and user-friendly tool that makes stunning molecular visuals in just minutes. 1. CRISPR-Cas9 Complex with DNA (PDB: 5Y36) This visualization showcases the famous CRISPR-Cas9 complex bound to DNA. By now, you’ve likely heard about CRISPR technologies and their revolutionary role in gene editing. Here, you get a glimpse of the molecular machinery in action—a frame of this groundbreaking gene-editing tool at the molecular level. 2. COVID-19 Spike Protein and ACE2 Receptor Binding (PDB: 6M0J) Next is the binding of the COVID-19 spike protein to the human ACE2 receptor. This structure, solved early in the pandemic using crystallography and cryo-EM techniques, revealed the molecular mechanism of viral entry. This visualization holds special significance for medicinal chemists working to design compounds ...
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Interactive Protein-Ligand Complexes for pan MTBCAs Inhibitor - Compound 5

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Interactive Protein-Ligand Viz for pan best MTβCAs Inhibitor: Compound 5 Compound 5 interacting with MTβCA1 (docking score: -5.76 | predicted pKi: 5.83 | experimental pki: 7.7) Compound 5 interacting with MTβCA2 (docking score: -21.41 | predicted pKi: 5.88 | experimental pki: 7.12) Compound 5 interacting with MTβCA3 (docking score: -26.751 | predicted pKi: 4.73 | experimental pki: 7.48)
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Interactive Network Visualisation

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Greetings! This page features an interactive network visualization to enhance understanding of compound, gene, and pathway interactions.  You can explore two network views (toggle using the " Network " selector):  1. Complete Network: Displays the entire compound - gene - pathway network.  2. Tuberculosis Interaction Subnetwork: Focuses on interactions specifically related to tuberculosis. Tap on this icon to visualize clearly. Feel free to play around.
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Basic work flow to build classification QSAR models

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Tutorial for building QSAR Models in KNIME: Part 1 In this blog post, I’ll guide you through the process of building QSAR (Quantitative Structure-Activity Relationship) models using the KNIME platform. Before starting, make sure you’ve installed the required cheminformatics nodes. If you need help with that, you can follow this video  or video for instructions. We will be using combination of native knime and cheminfomatics nodes. Once everything is set up, we can dive into preparing your bioactivity dataset and normalizing structures. Let’s get started! Preparing Your Bioactivity Dataset for Machine Learning In machine learning, high-quality data is crucial to achieving good model performance. The phrase " garbage in , garbage out " is particularly true here, so it’s essential to take the time to clean and normalize your dataset. For this tutorial, we are going to use the bioactivity dataset for carbonic anhydrase 9, with chembl ID:  CHEMBL3594   Here’s how you can prep...
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Art of virtual screening : Exploration and navigation of vast chemical spaces

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Virtual screening is like searching for a needle in a haystack, where the needle represents a potential inhibitor within a vast chemical space. It serves as a guide, helping researchers navigate this ever-expanding chemical universe to find compounds with optimal drug-like properties, favorable pharmacokinetics, and similarity to known active compounds in both 2D and 3D. It’s akin to piloting a shuttle through nearby clusters of molecules that show promise for a target or a group of targets. The total chemical space is staggeringly vast—estimated to be on the order of 10^60 molecules if one only considers combinations of carbon, oxygen, nitrogen, and hydrogen. This immense size makes it impossible to explore entirely, but typical chemical libraries used in virtual screening contain about 10^6 compounds, allowing researchers to focus on the most promising regions of this space. However, even with millions of molecules available, these libraries still leave much of the chemical space une...
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Location: C5F9+GM New Delhi, Delhi, India
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Sagar Singh Shyamal

Venturing into the domain of computational chemistry, with focus on guiding research with data-driven approaches.