# Deep Origin - llms.txt
# Markdown versions of all pages for AI agents and LLMs
# Base URL: https://deeporigin.com

# About Deep Origin
Deep Origin is a computational drug discovery company that builds AI and physics-based tools
to accelerate small molecule drug discovery. Founded by Michael Antonov (co-founder of Oculus)
and Dr. Garegin Papoian, we combine molecular simulation with machine learning to help
scientists find drugs faster.

# Main sections
- /index.md - Homepage
- /about.md - About the company and team
- /resources.md - Blog posts, papers, and events
- /api.md - API access for developers
- /balto-ai-assistant-for-drug-discovery.md - Balto AI assistant
- /glossary/*.md - Drug discovery glossary terms

# All available markdown files
- /about.md
- /academic-posters/accelerating-drug-discovery-with-physics-informed-machine-learning.md
- /academic-posters/addressing-drug-discovery-challenges-with-a-multiscale-molecular-modeling-pipeline.md
- /academic-posters/discovering-novel-synthetic-lethal-pairs-with-large-scale-cellular-simulations.md
- /academic-posters/implications-of-protein-dynamics-for-design-of-protacs-and-molecular-glues.md
- /academic-posters/practical-and-accurate-free-energy-calculations-using-neural-network-potentials.md
- /ai-scientist/endometriosis-targets.md
- /api-waitlist.md
- /api.md
- /balto-ai-assistant-for-drug-discovery.md
- /blog/a-blind-spot-in-drug-discovery-pocket-finding.md
- /blog/accelerated-computing-is-the-future-of-genomics.md
- /blog/ai-in-biology-could-data-hygiene-be-holding-you-back.md
- /blog/alphafold-3-exciting-advance-yet-unresolved-major-issues-remain.md
- /blog/announcing-deep-origin-os-beta.md
- /blog/arpa-h-award-to-replace-animal-testing.md
- /blog/benchmarking-and-development-of-ai-based-agentic-systems-for-autonomous-drug-discovery.md
- /blog/biosimai-merger.md
- /blog/building-operating-systems-for-science-with-docker.md
- /blog/deep-origin-and-nvidia-help-researchers-save-time-and-money-by-bringing-gpu-accelerated-genomics-tools-to-nextflow.md
- /blog/deep-origin-congratulates-isomorphic-labs-on-catching-up.md
- /blog/deep-origin-data-hub-building-frictionless-machines-for-the-life-sciences.md
- /blog/deep-origin-launches-first-and-only-drug-discovery-assistant-with-conversational-ai-interface-and-top-docking-technology.md
- /blog/docking-and-virtual-screening-in-drug-discovery-finding-the-right-hit.md
- /blog/dodock-doscore-closing-the-generalization-gap.md
- /blog/drug-discovery-ai-hype-and-reality-three-scientists-go-on-a-hike.md
- /blog/finally-a-useful-ai-assistant-for-drug-discovery-meet-balto.md
- /blog/finding-promising-molecules-and-biological-background-with-balto.md
- /blog/formic-labs-is-now-deep-origin.md
- /blog/how-best-to-build-a-virtual-cell-and-make-sure-its-useful.md
- /blog/jpm-25-from-the-trenches-ai-in-biotech-gets-tactical.md
- /blog/life-science-software-landscape.md
- /blog/out-of-the-box-genai-for-medicinal-chemistry.md
- /blog/tim-foley-joins-deep-origin-as-chief-commercial-officer.md
- /blog/we-built-a-98-accurate-full-molecule-data-extractor-for-pdfs-now-you-can-use-it.md
- /blog/we-spill-the-beans-deep-origins-ai-and-physics-based-models-for-drug-discovery.md
- /blog/where-docking-and-virtual-screening-drop-the-ball-in-drug-discovery.md
- /blog/why-are-bioinformatics-workflows-different.md
- /careers.md
- /contact-us.md
- /cookies.md
- /ddc.md
- /do-patent.md
- /do-studio.md
- /docking-benchmark.md
- /docking.md
- /events/deep-origin-challenge-2025.md
- /events/getting-started-with-computational-drug-discovery.md
- /events/getting-your-life-science-data-ready-for-the-ai-era.md
- /events/useful-generalization-is-the-benchmark-that-matters.md
- /events/variant-calling-with-nvidia-parabricks-and-gatk.md
- /fep.md
- /glossary.md
- /glossary/3d-qsar.md
- /glossary/admet-predictions.md
- /glossary/bioisosteres.md
- /glossary/biologics.md
- /glossary/chemical-fingerprints.md
- /glossary/chemical-libraries.md
- /glossary/chemical-reactivity.md
- /glossary/chemical-space.md
- /glossary/cheminformatics.md
- /glossary/clustering-analysis.md
- /glossary/covalent-docking.md
- /glossary/de-novo-drug-design.md
- /glossary/density-functional-theory-dft.md
- /glossary/docking.md
- /glossary/drug-resistance.md
- /glossary/electrostatic-potential-maps.md
- /glossary/energy-minimization.md
- /glossary/ensemble-based-virtual-screening.md
- /glossary/ensemble-docking.md
- /glossary/epigenetic-targets.md
- /glossary/force-fields.md
- /glossary/fragment-based-drug-design-fbdd.md
- /glossary/free-energy-calculations.md
- /glossary/high-throughput-screening-hts.md
- /glossary/hit-to-lead-h2l-optimization.md
- /glossary/homology-modeling.md
- /glossary/ligand-efficiency-le.md
- /glossary/ligand.md
- /glossary/lipophilicity.md
- /glossary/metadynamics.md
- /glossary/mm-pbsa-and-mm-gbsa.md
- /glossary/molecular-descriptors.md
- /glossary/molecular-dynamics-md-simulations.md
- /glossary/molecular-mechanics-mm.md
- /glossary/pharmacophore-modeling.md
- /glossary/polypharmacology.md
- /glossary/protein-ligand-interactions.md
- /glossary/protein-protein-interactions-ppis.md
- /glossary/qsar-quantitative-structure-activity-relationship.md
- /glossary/quantum-mechanics-molecular-mechanics-qm-mm.md
- /glossary/reactive-oxygen-species-ros.md
- /glossary/retrosynthetic-analysis.md
- /glossary/smiles-simplified-molecular-input-line-entry-system.md
- /glossary/structure-based-drug-design-sbdd.md
- /glossary/therapeutic-index.md
- /glossary/thermodynamic-cycles.md
- /glossary/watermap.md
- /index.md
- /interstellar-transmission.md
- /msa.md
- /news/arpa-h-award-to-replace-animal-testing.md
- /news/biosimai-merger.md
- /news/computational-platform-rationalizes-molecular-glue-dlbcl.md
- /news/deep-origin-congratulates-isomorphic-labs-on-catching-up.md
- /news/deep-origin-launches-first-and-only-drug-discovery-assistant-with-conversational-ai-interface-and-top-docking-technology.md
- /news/deep-origin-promotes-natalie-ma-phd-to-chief-business-officer.md
- /news/formic-labs-is-now-deep-origin.md
- /news/tim-foley-joins-deep-origin-as-chief-commercial-officer.md
- /news/virtual-screening-architecture-100-fold-hit-rate.md
- /newsletter.md
- /papers/a-bivalent-molecular-glue-linking-lysine-acetyltransferases-to-oncogene-induced-cell-death.md
- /papers/can-ai-agents-design-and-implement-drug-discovery-pipelines.md
- /papers/deep-mutational-scanning-reveals-egfr-mutations-conferring-resistance-to-the-4th-generation-egfr-tyrosine-kinase-inhibitor-blu-945.md
- /papers/overcoming-the-accuracy-generalization-tradeoff-in-docking-and-scoring-for-prospective-virtual-screening.md
- /partnerships.md
- /platform.md
- /press-mention/ashot-papoyan-advances-biotech-in-us-and-armenia.md
- /press-mention/building-oculus-innovation-grit-the-2-billion-vr-revolution-michael-antonov-part-2-4.md
- /press-mention/can-ai-shrink-drug-development-timelines-for-endometriosis.md
- /press-mention/debugging-aging-how-a-vr-pioneer-is-revolutionizing-longevity-michael-antonov-part-3-4.md
- /press-mention/deep-origin-partners-with-accuknox-for-cloud-security.md
- /press-mention/deep-origins-balto-ai-assistant-offers-bespoke-drug-discovery-tools-via-a-chat-interface.md
- /press-mention/from-scientist-to-startup-founder-building-the-virtual-cell-for-drug-discovery.md
- /press-mention/ginkgo-bioworks-partners-on-deep-origin-led-team-to-develop-new-tools-for-predicting-drug-safety.md
- /press-mention/how-biotech-will-shape-our-future-on-mars-and-beyond-ft-natalie-ma.md
- /press-mention/michael-antonov-from-virtual-world-builder-to-real-world-drug-designer.md
- /press-mention/simulating-life-accelerating-discovery-deep-origins-biotech-vision-michael-antonov-part-4-4.md
- /press-mention/simulating-life-with-ai-a-new-era-in-biology-with-michael-antonov-natalie-ma-from-deep-origin.md
- /press-mention/the-borrowed-computer-that-built-oculus---an-unlikely-biotech-journey-michael-antonov-part-1-4.md
- /press-mention/why-deep-origin-is-betting-on-both-physics-and-ai-for-drug-discovery-ep-132.md
- /press-mention/will-oculus-co-founder-be-able-to-simulate-biology-next.md
- /pricing.md
- /privacy.md
- /request-access.md
- /request-outlicensing.md
- /request-partnership-consultation.md
- /resources.md
- /security.md
- /software-licensing-agreement.md
- /subscriber-credits-addendum.md
- /team-member/akash-guru.md
- /team-member/albert-mkrtchyan.md
- /team-member/aleksandr-kaminskii.md
- /team-member/andrew-mochalskyy.md
- /team-member/aram-bughdaryan.md
- /team-member/aram-davtyan.md
- /team-member/aram-gharibyan.md
- /team-member/arman-fahradyan.md
- /team-member/arman-simonyan.md
- /team-member/armen-davtyan.md
- /team-member/armen-harutyunyan-ph-d.md
- /team-member/arsen-sargsyan.md
- /team-member/artur-hakobyan.md
- /team-member/ashot-papoyan.md
- /team-member/audrey-howell.md
- /team-member/audrey.md
- /team-member/ben-siranosian.md
- /team-member/bilal-shaikh.md
- /team-member/edgar-davtyan.md
- /team-member/elin-barnes.md
- /team-member/eric-dobroveanu.md
- /team-member/erik-arabyan.md
- /team-member/gagik-navasardyan.md
- /team-member/garegin-papoian.md
- /team-member/garik-petrosyan.md
- /team-member/gor-lavchyan.md
- /team-member/grigor-arakelov.md
- /team-member/hasmik-mnatsakanyan.md
- /team-member/hayk-saribekyan.md
- /team-member/henk-campher.md
- /team-member/jagdish-repaswal.md
- /team-member/james-komianos.md
- /team-member/jason-sunardi.md
- /team-member/jignesh-parmar-ph-d.md
- /team-member/kate.md
- /team-member/kenny-williams.md
- /team-member/khachik-smbatyan.md
- /team-member/khoren-petrosyan.md
- /team-member/laion-azeredo.md
- /team-member/laura-fornshell.md
- /team-member/lev-tsidilkovski.md
- /team-member/matt-shlosberg.md
- /team-member/max-ratnikov.md
- /team-member/max.md
- /team-member/merrill-cook.md
- /team-member/merrill.md
- /team-member/michael-antonov.md
- /team-member/movses-aghekyan.md
- /team-member/narek-ginoyan.md
- /team-member/natalie-ma.md
- /team-member/nelly-vardanyan.md
- /team-member/nimi-vashi.md
- /team-member/oliver-purcell.md
- /team-member/paul-lang.md
- /team-member/sergio-miguel-santos-ph-d.md
- /team-member/sevak-abrahamyan.md
- /team-member/shivani-puri.md
- /team-member/srinivas.md
- /team-member/stepan-kuznetsov.md
- /team-member/steve-cheney.md
- /team-member/tigran-a.md
- /team-member/tigran-abramyan.md
- /team-member/tigran.md
- /team-member/tim-foley.md
- /team-member/tsolak.md
- /team-member/vahagn-altunyan.md
- /team-member/vahram-arakelov.md
- /team-member/victorien-delannee-ph-d.md
- /team-member/vito-spadavecchio.md
- /team-member/vito.md
- /team-member/vladimir-aleksenko.md
- /team-member/yeva.md
- /terms.md
- /validated-assets.md

# Usage
Each HTML page has a corresponding .md file at the same path.
Example: /blog/my-post/ -> /blog/my-post.md

# Contact
For API access: https://deeporigin.com/api-waitlist
General inquiries: https://deeporigin.com/contact-us