Pharmacelera

🎄 Wishing you a joyful and relaxing holiday season! 🎄 #happyholidays #happynewyear #Pharmacelera

Using 3D Methods for Virtual Screening?? Here are key insights from our findings on query molecule conformations: • Carefully consider the query molecule conformation: Its selection plays a critical role in the identification of novel compounds, especially when aiming for greater chemical diversity. A 2D bias in the benchmarking set can undermine the impact of 3D conformations on virtual screening (VS) performance. • Address chemical diversity in internal validations: If your goal is to recover active compounds with high chemical diversity compared to the query molecule, ensure your metrics account for this challenge. • Leverage energy-minimized conformations: When targeting compounds with similar scaffolds, choosing the energy-minimized conformation of the query molecule can be beneficial, as it aligns the conformational space between the query and screened compounds due to shared chemical features. Compound libraries normally include minimized structures in a gas phase or solvent without target information. • Use X-ray conformations for specific cases: Consider X-ray conformations when the query molecule’s conformation is shaped by the binding pocket’s topology or specific interactions, as these may better reflect the bioactive state. Learn more about our study at: https://lnkd.in/deHzprHi or feel free to reach out to authors Javier Vázquez Lozano or Enric Herrero. . What’s your experience with query conformations in 3D virtual screening? Let’s discuss it! #VirtualScreening #3DMethods #DrugDiscovery #MolecularModeling #PharmaceuticalResearch #ChemistryInnovation #ComputationalChemistry #ScientificResearch #QueryOptimization

🚀🛠️ A new standardized protocol for the preparation of large 3D fully enumerated compound libraries In virtual screening, the quality of the 3D library is critical to identifying potent, selective ligands. But preparing these libraries isn’t straightforward, for example, a single 2D molecule can exist in multiple protomeric and tautomeric forms at a given pH. We’ve developed a protocol integrating internal scripts and PharmScreen® software for preparing 3D libraries tailored for LBVS and SBVS. Applied to the Enamine Screening Collection (4.4M compounds), it delivers: - 270M conformers for LBVS. - 7.9M stereoisomers for SBVS. The protocol isn't just limited to Enamine’s collection. We’ve successfully extended it to other large commercial libraries, such as Molport Screening Compounds. For projects requiring a more targeted approach, our protocol can filter 3D libraries based on drug-like properties. With our standardized protocol and PharmScreen®’s cutting-edge capabilities, we offer one of the largest and most up-to-date 3D screening libraries tailored to your drug discovery needs More details about our standardized protocol are available on our blog https://lnkd.in/dUf9vR5j Let’s take your CADD projects to the next level! #DrugDiscovery #VirtualScreening #PharmScreen #3DLibrary #CADD #LifeSciences

🚀 At #Pharmacelera, we push innovation to the edge with cutting-edge drug design technologies. We leverage Computational Aided Drug Design, Artificial Intelligence, and High-Performance Computing to help you discover transformative therapies for unmet medical needs. 💡🧬 Our technologies PharmScreen® and exaScreen® unlock hidden chemical novelty and diversity when identifying new hits, while PharmQSAR® drives the lead optimization process using unique 3D QM-based descriptors. Our tools support scientists and companies in creating effective treatments for the most complex healthcare challenges. 🧪🌐 📩 Contact us at contact@pharmacelera.com and be sure to visit our website to learn more about how we can support your journey in drug discovery: www.pharmacelera.com   #DrugDiscovery #AIinHealthcare #HighPerformanceComputing #ComputationalChemistry #Innovations #drugdiscovery #artificialintelligence #ai

The success of a ligand-based virtual screening campaign relies on their molecular descriptors, in this sense, Quantum Mechanics (QM)⚛️offer higher accuracy by capturing detailed electronic properties, the influence of 3D conformation, and key interactions that classical descriptors often overlook. Pharmacelera´s property molecular descriptors exploit self-consistent reaction fields methods to define hydrophobic topologies from atomic contributions. Our unique descriptors are calculated using accurate QM methods ⚛️, through the Recife Model 1 (RM1) parametrization of the Miertus Scrocco Tomassi (MST) model, which is known to be a reference method due to its good balance between accuracy and calculation time. However, QM calculations⚛️are still time-consuming, especially for huge chemical spaces.  To handle this challenge, our team has developed a Machine Learning model for predicting atomic logP, to determine if exploring huge chemical spaces in a reduced amount of time is possible. Our model includes physical descriptors (ex. topological, steric, and electrostatic descriptors)⚛️, transferring information about the 3D environment of the atom to the model. The precise description of each atom gave us the possibility to develop and validate a model able to predict 3D atomic contributions to logP values with an R^2 >0.9 for any kind of neutral drug-like molecule 2.000 times faster than the calculations using the RM1 parametrization (see graphics (A) and (B)) Using this atomic description, we have accurately extended it to predict other atomic properties. For example, graph (C) shows the excellent results obtained for Mulliken Charges derived from Density Functional Theory calculations from the QMUGs library.  #DrugDiscovery #QuantumMechanics #VirtualScreening #MachineLearning #MolecularDescriptors #PredictiveModeling #Pharmacelera #ComputationalChemistry #AI 

🚀 Pharmacelera’s Flexible Deployment Options 🚀 We understand that each project and organization has unique requirements when it comes to drug discovery and computational chemistry. That’s why we offer diverse deployment options tailored to meet your needs. Whether you're focused on optimizing workflows, accessing extensive molecular libraries, or running large-scale calculations, we’ve got you covered! Explore how these flexible deployment options can accelerate and facilitate your drug discovery process. For more information, feel free to reach out to contact@pharmaceelera.com #Pharmacelera #DrugDiscovery #drugdevelopment #ComputationalChemistry #DeploymentOptions #MolecularModeling #KNIME #API #Docker #MPI #molXplore #InnovationInPharma  

Extract the hidden chemical novelty and diversity contained in your Corporate chemical space using 3D QM-based descriptors! Turn your in-house validated collection of building blocks and chemical reactions into a unique ultra-large chemical space searchable with our breakthrough exaScreen® technology. exaScreen-intra is a newly developed functionality that will allow you to convert, in a few steps, the Corporate chemical knowledge (your preferred building blocks and chemical reactions) into a unique chemical space, that is only accessible by you. Using our unique 3D molecular field descriptors based on quantum mechanics approaches (exaScreen) will help you reveal the needle in the haystack. Get the most out of your corporate library with exaScreen-intra! #drugdiscovery #exaScreen #exaScreenintra #computationalchemistry #artificialintelligence #ai 

As the #EuroQSAR conference concludes, we want to take a moment to acknowledge our talented young researchers for their continuous involvement and meaningful contributions to the field 👏🌟 They highlighted the key role of topological hydrophobic surfaces (at the quantum mechanics level) in ligand-protein interactions (Brian Medel Lacruz), in the mining of huge chemical spaces (Javier Vázquez Lozano), and in improving the results in QSAR studies (Ariadna Llop). We also want to acknowledge and thank the rest of our dedicated team for their support and collaboration in making this innovative science possible. If you didn't have the chance to connect with them during the conference, please feel free to reach out. We are always open to exploring new collaborations and discussions. Let's look forward to another year of innovative research! 🖥️👩🔬 #EuroQSAR #compchem #computationalchemistry #medicinalchemistry #drugdiscovery

Are you enjoying EuroQSAR so far? Wonderful! 🎉 🎉 🎉 We invite you to visit our scientific team at Booth 10. They are ready to discuss Pharmacelera’s latest innovations to support your drug discovery projects and explore potential collaboration opportunities. Don’t miss it out—stop by for a discussion! 🤝 💡 🚀 #EuroQSAR #compchem #computationalchemistry #medicinalchemistry #drugdiscovery

Only a few days left for #EuroQSAR! If you want to learn more about our later research and case studies, we invite you to visit the following posters: Monday 23rd: P151 - Hydrophobicity-driven scoring function for accurate assessment of ligand binding poses. Presented by Brian Medel Lacruz Tuesday 24th P092 - Ultra large virtual screening using 3D QM-derived hydrophobicity descriptors. Presented by Javier Vázquez Lozano P130 - Exploration of the SARS-CoV-2 major protease binding site with PharmQSAR. Presented by Ariadna Llop Want to learn more about Pharmacelera technologies and services? Visit us at booth 10! #compchem #computationalchemistry #medicinalchemistry #drugdiscovery