{
  "id": 634116,
  "title": "Ab initio side-chain sampling with PUD+ enables high-fidelity protein dynamics across AI-driven and classical simulations",
  "url": "https://urgent.news/2026/08/11/ab-initio-side-chain-sampling-with-pud-enables-high-fidelity-protein",
  "topic": "ai",
  "section": "AI",
  "published": "2026-08-11T00:00:00.000Z",
  "source": {
    "name": "bioRxiv",
    "slug": "biorxiv",
    "url": "https://www.biorxiv.org/content/10.64898/2026.08.10.743906v1?rss=1"
  },
  "original_language": "en",
  "account": "Molecular dynamics simulations rely heavily on the quality and breadth of ab initio data used to construct force fields, yet the exploration of side-chain conformational space has been underwhelming. This research explores the effects of comprehensive ab initio sampling of dipeptide conformations on force field accuracy and the predictive power of molecular dynamics simulations. The Protein Unit Dataset Plus, PUD+, is introduced - a dataset of 40 million quantum mechanically generated conformations that provide unparalleled coverage of both backbone and side-chain conformational space. ML force fields trained on PUD+ and used in AI2BMD simulations display enhanced energy and force prediction accuracy, capturing high-fidelity protein folding dynamics and the flexibility of long side-chain systems. Additionally, PUD+ is utilized to reparameterize the CMAP term of the classical ff19SB force field, resulting in improved representation of intrinsically disordered protein dynamics and IDP-ligand binding. The findings indicate that ab initio sampling of dipeptide side-chain conformations can result in high-fidelity modeling of protein dynamics across AI-driven and classical simulation methods.",
  "summary": "The fidelity of molecular dynamics (MD) simulations fundamentally depends on the quality and coverage of the ab initio data used to parameterize the underlying force field, yet the role of side-chain conformational space remains insufficiently explored. In this study, we systematically investigate how comprehensive ab initio sampling of dipeptide conformations - specifically targeting side-chain…",
  "key_points": [],
  "editors_take": null,
  "illustration": null,
  "coverage": {
    "outlets": 1,
    "also_reported_by": []
  },
  "ai_generated": true,
  "disclaimer": "Summaries, key points and the editor’s take are written by software from other outlets’ reporting and may contain errors — always check the linked original."
}