# Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

arXiv: https://arxiv.org/abs/2002.01563 · HTML: https://mlsanity.com/paper/2002.01563/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 27 Jan 2020.

## Built on by (most cited first, 6 of 6)

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- [Contrastive Learning of Coarse-Grained Force Fields](https://mlsanity.com/paper/2205.10861/) (2022)
- [Impact of Stop Sets on Stopping Active Learning for Text Classification](https://mlsanity.com/paper/2201.05460/) (2022)
- [DMInet: An Accurate and Highly Flexible Deep Learning Framework for Drug Membrane Interaction with Membrane Selectivity](https://mlsanity.com/paper/2105.13928/) (2021)
- [SupraTITO: Transferable Generative Molecular Dynamics for Supramolecular Systems](https://mlsanity.com/paper/2610.01381/) (2026)

## Abstract (arXiv)

Electronically-active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water soluble and biocompatible substrate. Nanoaggregate properties can be controlled by tuning core chemistry and peptide composition, but the sequence-structure-function relations remain poorly characterized. In this work, we employ coarse-grained molecular dynamics simulations within an active learning protocol employing deep representational learning and Bayesian optimization to efficiently identify molecules capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically-active π-cores. We consider the DXXX-OPV3-XXXD oligopeptide family, where D is an Asp residue and OPV3 is an oligophenylene vinylene oligomer (1,4-distyrylbenzene), to identify the top performing XXX tripeptides within all 203 = 8,000 possible sequences. By direct simulation of only 2.3% of this space, we identify molecules predicted to exhibit superior assembly relative to those reported in prior work. Spectral clustering of the top candidates reveals new design rules governing assembly. This work establishes new understanding of DXXX-OPV3-XXXD assembly, identifies promising new candidates for experimental testing, and presents a computational design platform that can be generically extended to other peptide-based and peptide-like systems.