introduction to the orion molecular design platform
TRANSCRIPT
Introduction to the Orion®Molecular Design Platform
Matt Geballe
VP of Product
Agenda
• OpenEye & Orion Intro
• Orion for Molecular Design
• Orion Platform
Stellar nursery NGC 2174
Scientific & computational molecular design leader for nearly 25 years
Pioneered Orion – The only cloud-native molecular design platform
Fast Facts
Founded: 1997HQ: Santa Fe, NM
Venture Capital Investment:
$0
~80 employees, privately held,
employee-owned
Develops and integrates innovative scientific methods
ApplicationsToolkits
Unmatched Combination of Computational Solutions, Scale
& Speed
OpenEye Consulting Partnerships & Engagements
A design partner in accelerating and advancing your molecular design projects
OpenEye accelerates molecular design by melding science, technology
Applications & Toolkits
Discovery Preclinical
Access scientific methods at scale and streamline project timelines
Billions of possible molecules &antibodies
Hundreds ofleads
Handful of candidates
Orion: The Intersection of Technology and Science
Orion is a molecular design platform that enables you to:
Key platform technology features:
Create and edit the application of the latest OpenEye and 3rd-party scientific methods
Calculate complex molecular modeling in minutes or hours instead of days
Analyze and aggregate datasets to streamline development process decisions and accelerate results for your end customers
Collaborate with teams and key stakeholders, seamlessly sharing data, managing projects, and getting a clearer view of your modeling efforts
• Scaleable high-speed search and calculation throughAmazon Web Services
• Analysis tools
• Method development environment
• Annotating and sharing
• Unlimited storage and archiving
• World-class data security
Select an Orion platform option
Software-as-a-Service
Pricing per user via a pooled resource
Immediate turnkey solution for molecular discovery
Managed Service
Customized platform based on your company’s needs
Pricing per user or company via a dedicated stack
Ongoing user training, methods advice, and custom development
Standard set of high-value molecular design tools
Small Molecule Discovery Suite:
TODAYLarge-scale Virtual Screening
• 2D Similarity: Molecules as a Service (MaaS)
• 3D Similarity: FastROCS
• 3D Structure-based: Gigadock functionality
• Conformationally expanded compound libraries
Lead Optimization
• Automated pose testing via Molecular Dynamics
• Fragment replacement
• Quantum Mechanics
o Torsion scanning
o Tautomer evaluation
o Conformational profiling
FastROCSMaaS
Familiar OpenEye Apps & TKs• The OpenEye Package → Classic Floes
3D TanimotoSimilarity
EC2
FastROCS on Enamine REAL
• 3D Ligand-Based
• Search 2.5B• Time: ~30 mins.
• Cost: $50 - $200
+
Gigadock Enamine REAL
• Structure-Based
• Search 2.5B• Time: ~24 hours
• Cost : $10K – $30K
~100 ~10000
Billions
Well-known for Virtual Screening Calculations at Scale
Not just Virtual Screening Quantum Mechanics FloesFragmentation, Torsion Scanning,
GeomOpt, TautomersClassic FloesReplicating familiar
OpenEye Apps
Molecular Dynamics Floes
“Standard” MD, Solvate System, P-L MD and Analysis, RBFE
BioModeler FloesProtein Prep and
Modification, Loop Modeling, SiteHopper
NH
Generative FloesMMPs, 2D fragment
replacement, transform extraction, reaction-
based targeted libraries
®
Leverage Orion’s third-party methods integration
Open source MD engine supported in Orion’s MD Floes
package
Molecular Dynamics
Open source MD engine supported in
Orion’s MD Floes package
Quantum Mechanics
DBSCAN
HDBSCAN*
Variant of DBSCAN used in the MD package for pose clustering
as part of trajectory analysis
Clustering
Density-based clustering method used for 2D fingerprint-
based clustering
Add your own method
Interactive Search and Exploration
Molecules as a Service (MaaS)
FastROCSMacroMolecular
Data Service (MMDS)
Search Billions in Seconds with MaaS
• Blazing fast 2D, Substructure, Exact Structure, Title search
Exploration, Screening, Hit Expansion, and more…
Data Storage: Cloud-Scale and Flexible
• Project-centric Data Organization• Flexible, familiar scheme using folders
• Critical data shared across entire org
• Storage models designed for scale• Interactive analysis to massively
parallel I/O
• Generic data container• C++ implementation
• Uses beyond molecules
• Integrated into Orion UI
Orion Orchestrates Compute Resources
Live Costs
Elastic Hardware
• Workflow paradigm (cubes and floes)
• Powerful, cost-aware scheduling• Parallelization
• Fault tolerance
• Cycles
• Per-cube hardware requirements• Metrics
• On-demand & Spot
• Project & User Cost Accounting
Orion Software-as-a-Service (SaaS) vs. Managed Service
Feature/Functionality SaaS Managed Service
Access to OpenEye methods via Small Molecule Discovery Suite ✓ ✓
Upload and download data to Orion ✓ ✓
Leverage high security ✓ ✓
Use Standard Services: FastROCS/Molecules as a Service (MaaS)/Macromolecular Data Service (MMDS) ✓ ✓
Run OpenEye-provided methods ✓ ✓
Create and run custom methods
Customize services: FastROCS/Molecules as a Service (MaaS)/Macromolecular Data Service (MMDS) ✓
Create cubes, including third-party applications and toolkits ✓
Connect to corporate network, customize authentication (SSO), integrate with internal data and services ✓
Customize and configure available compute hardware ✓
Open Programming Platform
• Library of OpenEye Standard Cubes
• Python to its core
• Floes written in Python or assembled in UI
• Cubes are Python
• Third-party libraries
• PSI4, OpenMM, GROMACS, etc
• Scientific Python ecosystem
• Compiled binaries
• Commercial Code*
Easier Distributed Programming
• Simple extension from Serial to Parallel cube
• Scheduler handles:• scaling out parallelization
• Fault tolerance
• Flexibility and Control• Hardware Resources – CPU, RAM, Disk Space, GPU
• Parallelism – autoscaling, min/max parallel workers
• Group cubes to run in same process – avoid data serialization
• Data• Datasets – Results, set of OERecords, stored in DB
• Files – simple, flat files
• Collections – optimized for large, parallel I/O
Reader Cube
WriterCube
OMEGA Cube
Instance
Parallel OMEGA Cube
OMEGA Cube
Instance
OMEGA Cube
Instance
Develop & Test Locally
Orion Development Lifecycle
Package & Upload
Build
Cubes, Floes available in
Orion UI, API
Run
Publish to colleagues
Share
Orion
• Before Orion: 5-7 days– Very manual and time consuming (both setup and calculation)
• After Orion: 15 minutes- 1 hour
eMolecules(5M compounds)
Similaritysearch
2D fingerprint-based
FastROCS
GPU Ligand-based3D Shape
ROCS
3D Shape &chemical features
EON
3D Shape &ElectrostaticsAWS Storage
AWS GPUs
AWS CPUs
AWS CPUs
and Storage
AWS CPUs
InternalDockingAlgorithm
Docking
AWS CPUs
Not Just for Pushing the Envelope
Orion Client
• Orion Client: convenient way to interact with Orion via code• Python API, command line interface (OCLI)
• Handles authentication
• Place/retrieve data from Orion• Datasets, Collections, Files
• Run, monitor, upload Floes
• Data Organization
• Code works locally or in Orion• Heavily used in I/O Cubes, tests
Accelerating Science at OpenEye
®
Managed Service Overview
Integrating Orion
Standard features
Service data customization
Internalresourcesaccess
3rd party software integration
Curated Data Broker
Service Registry
AWS VPC
FastROCS
Corporate Compound
DB
MMDS
Internal Structure DB
Many ways to Integrate an in-house Service
• Query in Floe
MMP
Query
Results
Many ways to Integrate an in-house Service
• Query in Floe
• Externally Push/Pull data
Assay DBOrionClient Nightly Project Update
OERecords
Many ways to Integrate an in-house Service
• Query in Floe
• Externally Push/Pull data
• Externally Push, trigger Floe
HypothesisVirt Library
OrionClient
AI Design Engine
Project Hit Validation Floe
Integrate other tools and UIs with Orion
Orion
Small MoleculeDiscovery
Suite
Formulations Suite
AntibodyDiscovery
Suite
MaterialsScienceSuite
To Be Announced
Suite
Your OwnSuite
Core technologyplatform
Suites of scientificmethodsas turnkey solutions
The Orion Vision
®
Orion Is…
• A powerful, unified molecular design platformo OpenEye calculations and much more
o Large scale and small
• A Cloud-Native compute platform combining:o Large & diverse compute resources
o Immense data storage and parallel I/O
o Open programming platform
o Reproducible calculations
• Designed for integrationo 3rd Party Software
o OrionClient and ocli
o In-House Services and Data
