Benchmarking Generated Poses: How Rational is Structure-based Drug Design with Generative Models? Article Swipe
Charles B. Harris
,
Kieran Didi
,
Arian R. Jamasb
,
Chaitanya K. Joshi
,
Simon V. Mathis
,
Píetro Lió
,
Tom L. Blundell
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2308.07413
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2308.07413
Deep generative models for structure-based drug design (SBDD), where molecule generation is conditioned on a 3D protein pocket, have received considerable interest in recent years. These methods offer the promise of higher-quality molecule generation by explicitly modelling the 3D interaction between a potential drug and a protein receptor. However, previous work has primarily focused on the quality of the generated molecules themselves, with limited evaluation of the 3D molecule \emph{poses} that these methods produce, with most work simply discarding the generated pose and only reporting a "corrected" pose after redocking with traditional methods. Little is known about whether generated molecules satisfy known physical constraints for binding and the extent to which redocking alters the generated interactions. We introduce PoseCheck, an extensive analysis of multiple state-of-the-art methods and find that generated molecules have significantly more physical violations and fewer key interactions compared to baselines, calling into question the implicit assumption that providing rich 3D structure information improves molecule complementarity. We make recommendations for future research tackling identified failure modes and hope our benchmark can serve as a springboard for future SBDD generative modelling work to have a real-world impact.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- http://arxiv.org/abs/2308.07413
- https://arxiv.org/pdf/2308.07413
- OA Status
- green
- Cited By
- 18
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4385889851
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4385889851Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.48550/arxiv.2308.07413Digital Object Identifier
- Title
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Benchmarking Generated Poses: How Rational is Structure-based Drug Design with Generative Models?Work title
- Type
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preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-08-14Full publication date if available
- Authors
-
Charles B. Harris, Kieran Didi, Arian R. Jamasb, Chaitanya K. Joshi, Simon V. Mathis, Píetro Lió, Tom L. BlundellList of authors in order
- Landing page
-
https://arxiv.org/abs/2308.07413Publisher landing page
- PDF URL
-
https://arxiv.org/pdf/2308.07413Direct link to full text PDF
- Open access
-
YesWhether a free full text is available
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-
greenOpen access status per OpenAlex
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https://arxiv.org/pdf/2308.07413Direct OA link when available
- Concepts
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Benchmarking, Generative grammar, Computer science, Complementarity (molecular biology), Benchmark (surveying), Quality (philosophy), Machine learning, Artificial intelligence, Data science, Business, Epistemology, Geography, Geodesy, Marketing, Biology, Genetics, PhilosophyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
18Total citation count in OpenAlex
- Citations by year (recent)
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2025: 5, 2024: 11, 2023: 2Per-year citation counts (last 5 years)
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.Little | 93 |
| abstract_inverted_index.alters | 112 |
| abstract_inverted_index.design | 6 |
| abstract_inverted_index.extent | 108 |
| abstract_inverted_index.future | 162, 178 |
| abstract_inverted_index.models | 2 |
| abstract_inverted_index.recent | 23 |
| abstract_inverted_index.simply | 77 |
| abstract_inverted_index.years. | 24 |
| abstract_inverted_index.(SBDD), | 7 |
| abstract_inverted_index.between | 40 |
| abstract_inverted_index.binding | 105 |
| abstract_inverted_index.calling | 143 |
| abstract_inverted_index.failure | 166 |
| abstract_inverted_index.focused | 53 |
| abstract_inverted_index.impact. | 187 |
| abstract_inverted_index.limited | 63 |
| abstract_inverted_index.methods | 26, 72, 125 |
| abstract_inverted_index.pocket, | 17 |
| abstract_inverted_index.promise | 29 |
| abstract_inverted_index.protein | 16, 46 |
| abstract_inverted_index.quality | 56 |
| abstract_inverted_index.satisfy | 100 |
| abstract_inverted_index.whether | 97 |
| abstract_inverted_index.However, | 48 |
| abstract_inverted_index.analysis | 121 |
| abstract_inverted_index.compared | 140 |
| abstract_inverted_index.implicit | 147 |
| abstract_inverted_index.improves | 155 |
| abstract_inverted_index.interest | 21 |
| abstract_inverted_index.methods. | 92 |
| abstract_inverted_index.molecule | 9, 32, 68, 156 |
| abstract_inverted_index.multiple | 123 |
| abstract_inverted_index.physical | 102, 134 |
| abstract_inverted_index.previous | 49 |
| abstract_inverted_index.produce, | 73 |
| abstract_inverted_index.question | 145 |
| abstract_inverted_index.received | 19 |
| abstract_inverted_index.research | 163 |
| abstract_inverted_index.tackling | 164 |
| abstract_inverted_index.benchmark | 171 |
| abstract_inverted_index.extensive | 120 |
| abstract_inverted_index.generated | 59, 80, 98, 114, 129 |
| abstract_inverted_index.introduce | 117 |
| abstract_inverted_index.modelling | 36, 181 |
| abstract_inverted_index.molecules | 60, 99, 130 |
| abstract_inverted_index.potential | 42 |
| abstract_inverted_index.primarily | 52 |
| abstract_inverted_index.providing | 150 |
| abstract_inverted_index.receptor. | 47 |
| abstract_inverted_index.redocking | 89, 111 |
| abstract_inverted_index.reporting | 84 |
| abstract_inverted_index.structure | 153 |
| abstract_inverted_index.PoseCheck, | 118 |
| abstract_inverted_index.assumption | 148 |
| abstract_inverted_index.baselines, | 142 |
| abstract_inverted_index.discarding | 78 |
| abstract_inverted_index.evaluation | 64 |
| abstract_inverted_index.explicitly | 35 |
| abstract_inverted_index.generation | 10, 33 |
| abstract_inverted_index.generative | 1, 180 |
| abstract_inverted_index.identified | 165 |
| abstract_inverted_index.real-world | 186 |
| abstract_inverted_index.violations | 135 |
| abstract_inverted_index."corrected" | 86 |
| abstract_inverted_index.conditioned | 12 |
| abstract_inverted_index.constraints | 103 |
| abstract_inverted_index.information | 154 |
| abstract_inverted_index.interaction | 39 |
| abstract_inverted_index.springboard | 176 |
| abstract_inverted_index.themselves, | 61 |
| abstract_inverted_index.traditional | 91 |
| abstract_inverted_index.\emph{poses} | 69 |
| abstract_inverted_index.considerable | 20 |
| abstract_inverted_index.interactions | 139 |
| abstract_inverted_index.interactions. | 115 |
| abstract_inverted_index.significantly | 132 |
| abstract_inverted_index.higher-quality | 31 |
| abstract_inverted_index.recommendations | 160 |
| abstract_inverted_index.structure-based | 4 |
| abstract_inverted_index.complementarity. | 157 |
| abstract_inverted_index.state-of-the-art | 124 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 7 |
| citation_normalized_percentile |