Macs in Chemistry

Insanely Great Science

Searching Ultra large databases

 

There have been many estimates of the size of chemical space, an oft quoted number 1060 a number large enough to be effectively infinite.

At the beginning of December 2020 the NIH held a workshop looking at ultra large chemistry databases

Program Dec. 1, 2020

10:45 Susan Gregurick Welcome
11:00 Yurii Moroz Making virtual REAL: an Approach to Access Billions of Make-on-Demand Compounds
11:30 Daniel Kuhn Searching for novel chemical hit matter in large chemical spaces
12:00 Uta Lessel Boehringer Ingelheim Comprehensive Library of Accessible Innovative Molecules (BICLAIM)
12:30 Zhijie Liu Build & Explore Virtual Libraries for Drug Discovery Projects
1:00 Christos Nicolaou Idea2Data: Expediting Drug Discovery through Proximal Library Exploitation
1:30 Jason Deng & John Shirley Introduction to DEL informatics and Virtual Spaces at WuXi AppTec
2:00 Jennifer Elward Exploring GSK Space: Practical Application of Large Scale Virtual Screening
2:30 Venkatesh Mysore Screening Billions of Compounds on the AtomNet Model: Approaches and Future Directions

Dec. 2, 2020

11:00 Rick Stevens A Large-scale (4.2 Billion Molecules, 60TB) Compound Feature db for Deep Learning in Virtual Drug Screening
11:30 Vladimir Poroikov Revealing Antiviral Hits Among Billion Molecules with Ligand and Target-based Approaches
12:00 Jean-Louis Reymond The GDB Databases and Their Use for Drug Discovery
12:30 Matthias Rarey Combinatorial Approaches for Searching Synthetically Accessible Chemical Space
1:00 John Irwin Virtual Screening of Ultra Large Chemistry Databases
1:30 Gergely Zahoranszky-Kohalmi Integrated Computational Platform for Chemistry Automation
2:00 Tudor Oprea , The Art of Navigating in Chemical Bioactivity Space
2:30 Marc Nicklaus & Nadya Tarasova SAVI: Billions of Easily Synthesizable Compounds Generated with Expert-System Rules
3:00 Jim Brase ATOM – Scalable Deep Learning of Generative Models for Molecular Design Optimization

Dec. 3, 2020

11:00 Andrew Dalke & Brian Cole Compression of Chemfp Databases
11:30 Roger Sayle Advances in Searching Ultra-Large (100+ Billion Compound) Compound Chemical Databases: Arthor and SmallWorld
12:00 Christian Lemmen Efficient 3D Exploration of Multi-Billion Compound Spaces
12:30 Lutz Weber & Christoph Ruttkies SciWalker Next Generation - a Novel Comprehensive Semantic Chemistry Search Engine for Heterogeneous Documents and Databases
1:00 Wolf-Dietrich Ihlenfeldt Cloud Databases and Chemical Structure Searching
1:30 Evan Bolton Chemical Space is Infinite: How Can One Scale to Infinity While Still Being Usable/Useful
2:00 Ian Wetherbee & Stephen Boyer A Collaborative Database for Chemistry in Google BigQuery
2:30 Eugene Raush Chemical Substructure Search in Ultra Large Chemical Databases: Fast Virtual Screening with Rapid Isoster Discovery Engine (RIDE)
3:00 Mark McGann GigaDocking: Structure Based Virtual Screening of Billion of Molecules

There presentations are now available online. https://cactus.nci.nih.gov/presentations/NIHBigDB_2020-12/NIHBigDB.html.

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