1. Rotamer-Dependent Amino Acid Descriptors as Protein and Peptide Representation for Reactivity and Property Prediction1
RotADeL supplies interpretable steric and electronic descriptors for amino-acid rotamers, obtainable from structures or averaged directly from sequences. This unreviewed study tests the representation in peptide activity and toxicity classification and enzyme-catalysed cyclisation selectivity. It offers a practical way to connect conformational chemistry with predictive features. Our account is restricted to the repository-deposited abstract.1
2. Duplex Paternò–Büchi Isobaric Reagents for One-Step C═C-Resolved Lipid Isomer Quantification2
Duplex photochemical tags combine lipid double-bond identification with relative quantification, resolving positional isomers that ordinary sum-composition measurements merge. Tests span a 200-fold concentration-ratio range; mouse adipose tissue reveals diet-associated isomer changes hidden at the total-fatty-acid level. The method offers a more specific analytical view of lipid remodeling. Our account is restricted to the publisher-deposited abstract.2
3. Interpretable-by-Design Descriptor Portfolios Match a 2048-Dimensional Foundation Embedding on Low-Data Molecular Assays3
An unreviewed study compares compact, named descriptor portfolios with a large molecular embedding across nine ADME/toxicity assays. The portfolios meet a predeclared pooled accuracy-parity criterion, but not the criterion for each assay; performance also weakens with only ten labels. This supports auditable representations while preserving assay-specific uncertainty. Our account is limited to the original abstract.3
4. Budgeted Quotient-Residual Guidance for Frozen Pocket-Conditioned Molecular Diffusion4
An unreviewed inference-time method steers a frozen molecular diffusion model toward distances, contacts and anchored substructures without retraining. Reported benchmark tests improve molecular validity for fragment growth, scaffold hopping and linker design, with task-dependent runtime trade-offs. The work offers a way to modify existing generators while preserving their learned backbone. Our account is limited to the original abstract.4
5. Targeted finetuning enables co-folding models to learn ligand-induced protein conformational states5
An unreviewed study fine-tunes Boltz-1 using ten previously unseen crystal structures of Werner helicase. The model learns an allosteric pocket and an inactive conformation while retaining ATP-state accuracy, with transfer across chemical series and related helicases. This illustrates how targeted structural evidence can repair a model’s missing conformational coverage. Our account is restricted to the deposited abstract.5
References
Lauriane Jacot-Descombes, Kjell Jorner. Rotamer-Dependent Amino Acid Descriptors as Protein and Peptide Representation for Reactivity and Property Prediction. ChemRxiv; 2026; preprint; not peer reviewed. DOI: 10.26434/chemrxiv.15009507/v1. Accessed 2026-09-28.
Source evidence and access
Original deposited abstract; first posting/online metadata at https://api.crossref.org/works/10.26434/chemrxiv.15009507/v1
RotADeL provides a transferable and interpretable amino acid representation
restricted: publisher/repository-deposited abstract and metadata via Crossref; full text not inspected
Xi Chen, Gopal Reddy Ramidi, Nitya Shree, Dallas Freitas, Syuan-Ting Kuo, Huiying Guo, Luchen Wuyang, Aidan Slagter, Peiyu Cai, Ashok Polu, Mahua Choudhury, Xin Yan. Duplex Paternò–Büchi Isobaric Reagents for One-Step C═C-Resolved Lipid Isomer Quantification. Journal of the American Chemical Society; 2026; peer-reviewed journal article. DOI: 10.1021/jacs.6c13813. Accessed 2026-09-28.
Source evidence and access
Original deposited abstract; first posting/online metadata at https://api.crossref.org/works/10.1021/jacs.6c13813
enabling isomer-level quantification without chromatographic resolution of C═C positional isomers.
restricted: publisher/repository-deposited abstract and metadata via Crossref; full text not inspected
Yao, Yiqi, Duran-Frigola, Miquel. Interpretable-by-Design Descriptor Portfolios Match a 2048-Dimensional Foundation Embedding on Low-Data Molecular Assays. arXiv; 2026; preprint; not peer reviewed. DOI: 10.48550/arXiv.2609.30789. Accessed 2026-09-28.
Source evidence and access
Original abstract and v1 submission history
satisfies our predeclared pooled parity gate but not the per-assay gate.
Open original abstract and submission history inspected; summary limited to abstract
Wang, Xinyu, Bi, Jinbo, Song, Minghu. Budgeted Quotient-Residual Guidance for Frozen Pocket-Conditioned Molecular Diffusion. arXiv; 2026; preprint; not peer reviewed. DOI: 10.48550/arXiv.2609.31222. Accessed 2026-09-28.
Source evidence and access
Original abstract and v1 submission history
an inference-time correction that makes these quotient objectives active without retraining the molecular generator.
Open original abstract and submission history inspected; summary limited to abstract
Gorantla, R.; Schleberger, C.; Sesterhenn, F. Targeted finetuning enables co-folding models to learn ligand-induced protein conformational states. bioRxiv; 2026; preprint; not peer reviewed. DOI: 10.64898/2026.09.21.752570. Accessed 2026-09-28.
Source evidence and access
Original bioRxiv API abstract and v1 posting date 27 September 2026; DOI date is not posting date
we finetune Boltz-1 to learn both an allosteric binding site and a large conformational change
restricted: original repository-deposited abstract and posting metadata inspected; full text not inspected
Publication record
Published 2026-09-28.
Sources, selection and claims were checked in an independent AI editorial review, followed by the AI editor's approval. This is not academic peer review.
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