ArticleMolecular informatics2025
Navigating a 1E+60 Chemical Space of Peptide/Peptoid Oligomers.
Article in Molecular informatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- PepFoundry: A Pipeline for Building Machine-Learning Ready Representations of Nonstandard Peptides Containing Cycles, Non-natural Residues, Polymer Units, and More.Journal of chemical information and modeling · 2026Article
- Exploring and expanding the chemical multiverse of peptides.Chemical science · 2026Review
- Diffusion Models at the Drug Discovery Frontier: A Review on Generating Small Molecules Versus Therapeutic Peptides.Biology · 2025Review
- A View on Molecular Complexity from the GDB Chemical Space.Journal of chemical information and modeling · 2025Review
- Geographic-style maps with a local novelty distance help navigate in the materials space.Scientific reports · 2025Article
- Antimicrobial Peptide-Peptoid Macrocycles from the Polymyxin B2 Chemical Space.Angewandte Chemie (International ed. in English) · 2025Article
- Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World.Chemical research in toxicology · 2025Review
- Innovative perspectives on the discovery of small molecule antibiotics.npj antimicrobials and resistance · 2025Review
- Chemical space as a unifying theme for chemistry.Journal of cheminformatics · 2025Article
- Navigating a 1E+60 Chemical Space of Peptide/Peptoid Oligomers.Molecular informatics · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Herein we report a virtual library of 1E+60 members, a common estimate for the total size of the drug-like chemical space. The library is obtained from 100 commercially available peptide and peptoid building blocks assembled into linear or cyclic oligomers of up to 30 units, forming molecules within the size range of peptide drugs and potentially accessible by solid-phase synthesis. We demonstrate ligand-based virtual screening (LBVS) using the peptide design genetic algorithm (PDGA), which evolves a population of 50 members to resemble a given target molecule using molecular fingerprint similarity as fitness function. Target molecules are reached in less than 10,000 generations. Like in many journeys, the value of the chemical space journey using PDGA lies not in reaching the target but in the journey itself, here by encountering non-obvious analogs. We also show that PDGA can be used to generate median molecules and analogs of non-peptide target molecules.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.