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Showing 1–20 of 20 results
Advanced filters: Author: Olexandr Isayev Clear advanced filters
  • Computational modelling of chemical systems requires a balance between accuracy and computational cost. Here the authors use transfer learning to develop a general purpose neural network potential that approaches quantum-chemical accuracy for reaction thermochemistry, isomerization, and drug-like molecular torsions.

    • Justin S. Smith
    • Benjamin T. Nebgen
    • Adrian E. Roitberg
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-8
  • AQuaRef employs machine learning to refine protein structures from cryo-EM and X-ray data in Phenix. It achieves quantum-level precision, improving model geometry and fit to the data while reducing overfitting.

    • Roman Zubatyuk
    • Malgorzata Biczysko
    • Pavel V. Afonine
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-12
  • Machine learning methods can be useful for materials discovery; however certain properties remain difficult to predict. Here, the authors present a universal machine learning approach for modelling the properties of inorganic crystals, which is validated for eight electronic and thermomechanical properties.

    • Olexandr Isayev
    • Corey Oses
    • Alexander Tropsha
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-12
  • As quantum mechanics marks its centennial, machine learning interatomic potentials are emerging as transformative tools bridging quantum accuracy with classical efficiency. This Perspective explores their evolution in terms of accuracy, efficiency, interpretability and generalizability challenges.

    • Bhupalee Kalita
    • Hatice Gokcan
    • Olexandr Isayev
    Reviews
    Nature Computational Science
    Volume: 5, P: 1120-1132
  • Computer algorithms can be used to analyse text to find semantic relationships between words without human input. This method has now been adopted to identify unreported properties of materials in scientific papers.

    • Olexandr Isayev
    News & Views
    Nature
    Volume: 571, P: 42-43
  • Quantum mechanical calculations of molecular ionized states are computationally quite expensive. This work reports a successful extension of a previous deep-neural networks approach towards transferable neural-network models for predicting multiple properties of open shell anions and cations.

    • Roman Zubatyuk
    • Justin S. Smith
    • Olexandr Isayev
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-11
  • Artificial intelligence is combined with quantum mechanics to break the limitations of traditional methods and create a new general-purpose method for computational chemistry simulations with high accuracy, speed and transferability.

    • Peikun Zheng
    • Roman Zubatyuk
    • Pavlo O. Dral
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-13
  • Statistical tools based on machine learning are becoming integrated into chemistry research workflows. We discuss the elements necessary to train reliable, repeatable and reproducible models, and recommend a set of guidelines for machine learning reports.

    • Nongnuch Artrith
    • Keith T. Butler
    • Aron Walsh
    Comments & Opinion
    Nature Chemistry
    Volume: 13, P: 505-508
  • Atomistic simulations have a broad range of applications from drug design to materials discovery. Machine learning interatomic potentials (MLIPs) have become an efficient alternative to computationally expensive ab initio simulations. Now a general reactive MLIP (called ANI-1xnr) has been developed and validated against a broad range of condensed-phase reactive systems.

    • Shuhao Zhang
    • Małgorzata Z. Makoś
    • Justin S. Smith
    ResearchOpen Access
    Nature Chemistry
    Volume: 16, P: 727-734
  • The IDG-DREAM Challenge carried out crowdsourced benchmarking of predictive algorithms for kinase inhibitor activities on unpublished data. This study provides a resource to compare emerging algorithms and prioritize new kinase activities to accelerate drug discovery and repurposing efforts.

    • Anna Cichońska
    • Balaguru Ravikumar
    • Tero Aittokallio
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-18
  • Deep generative neural networks are increasingly exploited for drug discovery, but often the majority of generated molecules are predicted to be inactive. Here, an optimized protocol for generative models with reinforcement learning is derived and applied to design potent epidermal growth factor inhibitors.

    • Maria Korshunova
    • Niles Huang
    • Olexandr Isayev
    ResearchOpen Access
    Communications Chemistry
    Volume: 5, P: 1-11
  • Resistance to first line treatment is a major hurdle in cancer treatment, that can be overcome with drug combinations. Here, the authors provide a large drug combination screen across cancer cell lines to benchmark crowdsourced methods and to computationally predict drug synergies.

    • Michael P. Menden
    • Dennis Wang
    • Julio Saez-Rodriguez
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-17
  • GPUs, which are highly parallel computer processing units, were originally designed for graphics applications, but they have played an important role in accelerating the development of deep learning methods. In this Review, Pandey and colleagues summarize how GPUs have advanced machine learning in the field of drug discovery.

    • Mohit Pandey
    • Michael Fernandez
    • Artem Cherkasov
    Reviews
    Nature Machine Intelligence
    Volume: 4, P: 211-221
  • Advances with deep learning, the growth of databases of molecules for virtual screening and improvements in computational power have supported the emergence of a new field of quantitative structure–activity relationship (QSAR) modelling applications that Tropsha et al. term ‘deep QSAR’. This article discusses key advances in the field, including deep generative and reinforcement learning approaches in molecular design, deep learning models for synthetic planning, and the use of deep QSAR models in structure-based virtual screening.

    • Alexander Tropsha
    • Olexandr Isayev
    • Artem Cherkasov
    Reviews
    Nature Reviews Drug Discovery
    Volume: 23, P: 141-155
  • The prediction of interatomic potentials by machine learning is a well developed method; however, interatomic potentials account for only the energies and atomic forces and neglect other essential chemical properties. This Review showcases how other properties of interest, such as atomic charges, dipole moments, long-range effects, bond orders and parameters of reduced Hamiltonians, can also be accurately predicted using machine learning models.

    • Nikita Fedik
    • Roman Zubatyuk
    • Sergei Tretiak
    Reviews
    Nature Reviews Chemistry
    Volume: 6, P: 653-672