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RESEARCH PAPER · Scientific Data · 2020

SAVI, in silico generation of billions of easily synthesizable compounds through expert-system type rules

Hitesh Patel, Wolf Dietrich Ihlenfeldt, Philip Neville Judson, Yurii S. Moroz, Yuri Pevzner, Megan L. Peach, Victorien Delannée, Nadya I. Tarasova, Marc C. Nicklaus

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SAVI, in silico generation of billions of easily synthesizable compounds through expert-system type rulesOriginalAccelerating high-throughput virtual screening through molecular pool-based active learning302Scaffold Embeddings: Learning the Structure Spanned by Chemical Fragments, Scaffolds and Compounds2FragNet, a Contrastive Learning-Based Transformer Model for Clustering, Interpreting, Visualizing, and Navigating Chemical Space24Report on an NIH Workshop on Ultralarge Chemistry Databases23Star-shaped molecules cross-bind to SARS-CoV2 spike α-helices in silico0National Institutes of Health (NIH) Workshop on Reaction Informatics7Star-shaped Triazine-derivatives: would they crossbind SARS-CoV-2 spike helices?8A practical guide to large-scale docking537Fully Automated Creation of Virtual Chemical Fragment Spaces Using the Open-Source Library OpenChemLib16Exploration of Ultralarge Compound Collections for Drug Discovery152Algorithm for the Pruning of Synthesis Graphs4Reaction SPL – extension of a public document markup standard to chemical reactions1Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets14Automatic Extraction of Reaction Templates for Synthesis Prediction1Analysing a billion reactions with the RInChI1Defining Levels of Automated Chemical Design44Rings in Clinical Trials and Drugs: Present and Future479Towards systematic exploration of chemical space: building the fragment library module in molecular property diagnostic suite14Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery25Roles and opportunities for machine learning in organic molecular crystal structure prediction and its applications18Deep generative molecular design reshapes drug discovery290Electrochemoinformatics as an Emerging Scientific Field for Designing Materials and Electrochemical Energy Storage and Conversion Devices—An Application in Battery Science and Technology24AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection33Global reactivity models are impactful in industrial synthesis applications15Navigating large chemical spaces in early-phase drug discovery64Correlation of binding site properties with chemistries used for generation of ultra-large virtual libraries.0New star-shaped ligands generated by evolutionary fitting the Omicron spike inner-cavity10Virtual screening of ultra-large chemical libraries identifies cell-permeable small-molecule inhibitors of a “non-druggable” target, STAT3 N-terminal domain17Computational approaches streamlining drug discovery1279Fast Substructure Search in Combinatorial Library Spaces11Keeping pace with the explosive growth of chemical libraries with structure‐based virtual screening37FP-MAP: an extensive library of fingerprint-based molecular activity prediction tools5DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening23Molecular Property Diagnostic Suite Compound Library (MPDS-CL): a structure-based classification of the chemical space5Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening1Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening2A Mechanism to Open Academic Chemistry to High-Throughput Virtual Screening3Integrating QSAR modelling and deep learning in drug discovery: the emergence of deep QSAR397Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening3Sample efficient reinforcement learning with active learning for molecular design55Ultra-Large-Scale Virtual Screening2Enumerable Libraries and Accessible Chemical Space in Drug Discovery4Database of 4 Million Medicinal Chemistry-Relevant Ring Systems14RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries7Correlation of protein binding pocket properties with hits’ chemistries used in generation of ultra-large virtual libraries3Neural Template Extraction - Learning the Language of SMIRKS0High Performance Binding Affinity Prediction with a Transformer-Based Surrogate Model3The Pan-Canadian Chemical Library: A Mechanism to Open Academic Chemistry to High-Throughput Virtual Screening11The IMS Library: from IN‐Stock to Virtual4Path Toward High-Throughput Synthesis Planning via Performance Benchmarking0The freedom space – a new set of commercially available molecules for hit discovery10Structure and dynamics in drug discovery81SAVI Space—combinatorial encoding of the billion-size synthetically accessible virtual inventory6Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging Targets7Ring systems in medicinal chemistry: A cheminformatics analysis of ring popularity in drug discovery over time21Freedom Space 3.0: ML-Assisted Selection of Synthetically Accessible Small Molecules6Generative AI for navigating synthesizable chemical space38Scaffold‐Based Libraries Versus Make‐on‐Demand Space: A Comparative Assessment of Chemical Content2SLICE (SMARTS and Logic In ChEmistry): fast generation of molecules using advanced chemical synthesis logic and modern coding style0Advances and perspectives in computer-assisted structure elucidation: a review3An overview of reaction outcome prediction with physics-based and data-driven methods2Yield Prediction of Organic Reactions in Biased Data Sets via Positive-Unlabeled Learning3Molecular Dynamics Workflows to Compute Large-Scale Sets of Absolute Binding Free Energies Aiding Drug Candidate and Binding Pose Selection2The (r)evolution of chemical space and molecular modeling: a time-resolved perspective2Big Data and Artificial Intelligence in Cancer Drug Discovery: Promise, Challenges, and Emerging Opportunities0

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  1. Accelerating high-throughput virtual screening through molecular pool-based active learning

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  2. Scaffold Embeddings: Learning the Structure Spanned by Chemical Fragments, Scaffolds and Compounds

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  3. FragNet, a Contrastive Learning-Based Transformer Model for Clustering, Interpreting, Visualizing, and Navigating Chemical Space

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  4. Report on an NIH Workshop on Ultralarge Chemistry Databases

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  5. Star-shaped molecules cross-bind to SARS-CoV2 spike α-helices in silico

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  6. National Institutes of Health (NIH) Workshop on Reaction Informatics

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  7. Star-shaped Triazine-derivatives: would they crossbind SARS-CoV-2 spike helices?

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  8. A practical guide to large-scale docking

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  9. Fully Automated Creation of Virtual Chemical Fragment Spaces Using the Open-Source Library OpenChemLib

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  10. Exploration of Ultralarge Compound Collections for Drug Discovery

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  11. Algorithm for the Pruning of Synthesis Graphs

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  12. Reaction SPL – extension of a public document markup standard to chemical reactions

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  13. Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets

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  14. Automatic Extraction of Reaction Templates for Synthesis Prediction

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  15. Analysing a billion reactions with the RInChI

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  16. Defining Levels of Automated Chemical Design

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  17. Rings in Clinical Trials and Drugs: Present and Future

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    Jonathan Shearer, José L. Castro, Alastair D. G. Lawson, Malcolm MacCoss, Richard D. Taylor

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  18. Towards systematic exploration of chemical space: building the fragment library module in molecular property diagnostic suite

    Molecular Diversity · 2022-08-04

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  19. Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery

    Journal of Chemical Information and Modeling · 2022-09-14

    Yuliana Zabolotna, Fanny Bonachéra, Dragos Horvath, Arkadii Lin, Gilles Marcou, Olga Klimchuk, Alexandre A. Varnek

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  20. Roles and opportunities for machine learning in organic molecular crystal structure prediction and its applications

    MRS Bulletin · 2022-10-01

    Rebecca J. Clements, Joshua Dickman, Jay Johal, Jennie Martin, Joseph Glover, Graeme Matthew Day

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  21. Deep generative molecular design reshapes drug discovery

    Cell Reports Medicine · 2022-10-27

    Xiangxiang Zeng, Fei Wang, Yuan Luo, Seung-Gu Kang, Jian Guo Tang, Felice C. Lightstone, Evandro Fei Fang, Wendy D. Cornell, Ruth Nussinov, Feixiong Cheng

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  22. Electrochemoinformatics as an Emerging Scientific Field for Designing Materials and Electrochemical Energy Storage and Conversion Devices—An Application in Battery Science and Technology

    Advanced Energy Materials · 2022-11-07

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  23. AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection

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  24. Global reactivity models are impactful in industrial synthesis applications

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  25. Navigating large chemical spaces in early-phase drug discovery

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  26. Correlation of binding site properties with chemistries used for generation of ultra-large virtual libraries.

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  27. New star-shaped ligands generated by evolutionary fitting the Omicron spike inner-cavity

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  28. Virtual screening of ultra-large chemical libraries identifies cell-permeable small-molecule inhibitors of a “non-druggable” target, STAT3 N-terminal domain

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  29. Computational approaches streamlining drug discovery

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  30. Fast Substructure Search in Combinatorial Library Spaces

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  31. Keeping pace with the explosive growth of chemical libraries with structure‐based virtual screening

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  32. FP-MAP: an extensive library of fingerprint-based molecular activity prediction tools

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  33. DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening

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  34. Molecular Property Diagnostic Suite Compound Library (MPDS-CL): a structure-based classification of the chemical space

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  35. Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening

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  36. Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening

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  37. A Mechanism to Open Academic Chemistry to High-Throughput Virtual Screening

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  38. Integrating QSAR modelling and deep learning in drug discovery: the emergence of deep QSAR

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  39. Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening

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  40. Sample efficient reinforcement learning with active learning for molecular design

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  41. Ultra-Large-Scale Virtual Screening

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  42. Enumerable Libraries and Accessible Chemical Space in Drug Discovery

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  43. Database of 4 Million Medicinal Chemistry-Relevant Ring Systems

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  45. Correlation of protein binding pocket properties with hits’ chemistries used in generation of ultra-large virtual libraries

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  47. High Performance Binding Affinity Prediction with a Transformer-Based Surrogate Model

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  48. The Pan-Canadian Chemical Library: A Mechanism to Open Academic Chemistry to High-Throughput Virtual Screening

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  50. Path Toward High-Throughput Synthesis Planning via Performance Benchmarking

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