Papers › ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids

ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids

6 Mar 2025arXiv:2503.05025archive 2025-07-28

Hannes Stark, Bowen Jing, Tomas Geffner, Jason Yim, Tommi Jaakkola, Arash Vahdat, Karsten Kreis

We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference time, we condition on ellipsoids that are hand-constructed, extracted from existing proteins, or from a statistical model, with each option unlocking new capabilities. Hand-specifying ellipsoids enables users to control the location, size, orientation, secondary structure, and approximate shape of protein substructures. Conditioning on ellipsoids of existing proteins enables redesigning their substructure's connectivity or editing substructure properties. By conditioning on novel and diverse ellipsoid layouts from a simple statistical model, we improve protein generation with expanded Pareto frontiers between designability, novelty, and diversity. Further, this enables sampling designable proteins with a helix-fraction that matches PDB proteins, unlike existing generative models that commonly oversample conceptually simple helix bundles. Code is available at https://github.com/NVlabs/protcomposer.

Code

Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.

Code Syntology ran Syntology

7 samples harvested; 5 ran; 0 honoured the contract we drafted; 2 have no recorded run. Read from Syntology's graph 2026-09-24; that is when this build read the record, not when the samples ran.

Licence: 0 of the 7 samples are pointer only, meaning Syntology does not serve that copy's text. This page shows no code text for any sample; each one links to its file in the repository.

Harvested from 2 repositories linked to this paper, official or community; each sample names its own and says which. “Ran” means the sample executed on a synthesized input. It does not mean the output is correct, and nothing here reproduces the paper's results. “Honoured” and “violated” refer to a contract Syntology drafted from the code itself; “our draft was wrong” and “fixture could not drive it” are failures of Syntology's instrument, not of the code.

Each sample ends with its code_sha256, Syntology's identity for that exact code. An agent fetches the stored sample with Syntology's MCP tool get_code(code_sha256="…") (how to connect); click an identity to copy that call.

Repository labels, per sample. official repository: The archive marks this repository official for the paper. named in the paper: The archive records that the paper mentions this repository; it is not marked official. community (archive-listed): In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper. found in paper text by Syntology: Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted. community: Not in the archive's code links for this paper; a community repository Syntology harvested. Samples from a repository marked official are listed first. Licence labels name the repository's licence as recorded at harvest. “Pointer only” means Syntology does not serve that copy's text, for one of four reasons: no licence file was found; the licence was not identified; the licence is recorded as permissive but that copy's record is not marked cleared; or the licence is outside the permissive list Syntology serves text under (MIT, Apache-2.0, BSD and similar). Some licences outside that list permit redistribution, such as WTFPL, and GPL-3.0 under its conditions; they are simply not on the list. Hover a licence label for the reason. File links open the file on GitHub at the default branch, which may have changed since the harvest.

Tasks

Results from the paper archive 2025-07-28

No leaderboard rows for this paper in the archive.

Methods

Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections