Evidence map›Paper›PMID 40894579›Full record

ArticlebioRxiv : the preprint server for biology2025

Conditional Protein Structure Generation with Protpardelle-1c.

Tianyu Lu, Richard Shuai, Petr Kouba, Zhaoyang Li, Yilin Chen, Akio Shirali, Jinho Kim, Po-Ssu Huang

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Tianyu LuDepartment of Bioengineering, Stanford University.ORCID 0000-0002-3365-1542
Richard ShuaiDepartment of Biophysics, Stanford University.ORCID 0000-0001-8375-8180
Petr KoubaCIIRC, Czech Technical University in Prague, Loschmidt Laboratories, Masaryk University.ORCID 0000-0002-9979-4159
Zhaoyang LiDepartment of Bioengineering, Stanford University.
Yilin ChenDepartment of Bioengineering, Stanford University.
Akio ShiraliDepartment of Chemical Engineering, Stanford University.
Jinho KimDepartment of Physics, Stanford University.
Po-Ssu HuangDepartment of Bioengineering, Stanford University.ORCID 0000-0002-7948-2895

Funding

Generative neural networks for structure-based antibody designR01GM147893 · NIGMS · STANFORD UNIVERSITY · PI Possu Huang · 2022 to 2026
$1.9M
NIGMS NIH HHS R01 GM147893
6 · The paper itself

Abstract

We present Protpardelle-1c, a collection of protein structure generative models with robust motif scaffolding and support for multi-chain complex generation under hotspot-conditioning. Enabling sidechain-conditioning to a backbone-only model increased Protpardelle-1c's MotifBench score from 4.97 to 28.16, outperforming RFdiffusion's 21.27. The crop-conditional all-atom model achieved 208 unique solutions on the La-Proteina all-atom motif scaffolding benchmark, on par with La-Proteina while having ~10 times fewer parameters. At 22M parameters, Protpardelle-1c enables rapid sampling, taking 40 minutes to sample all 3000 MotifBench backbones on an NVIDIA A100-80GB, compared to 31 hours for RFdiffusion.

Identifiers

PMID40894579
PMCPMC12393353

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

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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.