AlpTartici/inversefolddir

Inverse FoldDir

Structure-conditioned protein sequence design by Dirichlet flow matching.

Give it a protein backbone; it generates amino-acid sequences predicted to fold into that backbone. Supports full-sequence generation, fixed-residue inpainting, and soft residue-prior conditioning.

• Code: https://github.com/AlpTartici/inversefolddir
• License: MIT
• Architecture: SE(3)-equivariant GVP graph encoder + Dirichlet flow matching
• Parameters: 9.6M
• Input: protein backbone (.pdb or .cif); side chains not required
• Output: amino-acid sequence(s)

Quick start

git clone https://github.com/AlpTartici/inversefolddir.git
cd inversefolddir

python -m venv ifd-env && source ifd-env/bin/activate
pip install torch --index-url https://download.pytorch.org/whl/cpu
pip install -r requirements.txt

Download the checkpoint:

from huggingface_hub import hf_hub_download

path = hf_hub_download(
    repo_id="AlpTartici/inversefolddir",
    filename="inverse_folddir_model.pt",
)
print(path)

Design a sequence:

python training/inpainting.py \
    --pdb_input your_structure.pdb \
    --model /path/from/hf_hub_download \
    --mask-ratio 1.0 \
    --output-dir output/my_design

Read the result:

from inversefolddir_tools import load_results, write_fasta

r = load_results("output/my_design")
r.summary()
write_fasta(r, "design.fasta")

Full walkthrough: docs/GETTING_STARTED.md.

Design modes

Full generation — redesign every position:

--mask-ratio 1.0

Fixed-residue inpainting — preserve catalytic residues, disulfides, or interface positions while redesigning the rest:

--fixed-positions "C22,C96,W47"

Soft residue priors — bias positions toward a residue class without fixing them to one identity:

--soft-priors "34:polar, 57:metal_binding"

Positions are 1-indexed. Run python training/inpainting.py --list-residue-classes for the available classes.

Sampling settings

Architecture, graph featurization, and the flow's alpha grid are stored inside the checkpoint and read back automatically. Three things are not stored and take command-line defaults, which matters if you copy a command from elsewhere:

Setting	inpainting.py	sample.py	Default
Flow horizon	--t_max	--T	8.0
Step count	--steps	--steps	20
Sampling temperature	--flow_temp	--flow_temp	1.0

Note the horizon flag is spelled differently by the two entry points. This checkpoint was trained at t_max = 8; sampling at a longer horizon works and the c_factor table is rebuilt to cover it, but it is extrapolation beyond the trained range.

Training data

CATH 4.2, stock Ingraham splits, never re-split: 18,024 train / 608 validation / 1,120 test chains.

AlphaFold DB: 2,824,736 structures. Built from the Barrio-Hernandez et al. AFDB cluster release (2,302,907 clusters with at least two members); no clustering was run here, so there is no clustering threshold of ours to quote.

2,302,907  AFDB clusters (>= 2 members)
             pLDDT gate: representative > 70 AND cluster average > 70
             leakage removal (below)
1,211,316  usable clusters
             expanded to members
3,199,383  candidate structures
             per-structure gate: mean pLDDT >= 70, length <= 700 residues
2,824,736  structures used for training

Three separate pLDDT-70 gates, easy to conflate and worth stating apart: at the cluster level (representative and average pLDDT > 70), at the structure level (mean pLDDT >= 70), and again at load time per residue (residues below pLDDT 70 are chopped out; resulting contiguous segments shorter than 100 residues are discarded). The residues the model actually sees are therefore a subset of the structures counted above.

Leakage control

Held-out CATH chains were mapped to AFDB cluster representatives through SIFTS, and every cluster within Foldseek E-value < 0.1 of a held-out representative was removed in whole — members included, not just the matching representative. That excluded 8,190 representatives, removing 4,355 of the 1,215,671 pLDDT-passing clusters (0.358%).

Three things are worth knowing about that cutoff, because they are what makes it checkable rather than merely stated:

• It is 10x broader than the E < 0.01 used to build the AFDB clusters in the first place, and it removes whole clusters rather than single representatives.
• It is not load-bearing. Sweeping from "remove nothing detectable" to "remove any hit at all (E <= 10)" moves the amount removed only from 0.002% to 0.86% of training clusters. The corpus does not depend on a narrow band of benchmark-adjacent structures.
• What survives is normal for this benchmark. After filtering, no held-out CATH chain has a retained training cluster within E < 0.1, and 97.3% have no structurally detectable neighbour at all. Of the 43 residual neighbours, 13 sit at TM >= 0.5 — but CATH 4.2 itself places 51% of held-out chains within TM >= 0.5 of a CATH training chain (median 0.504, max 0.979). For 32 of the 39 at-risk chains, CATH's own training split already contains something at least as close.

Two holes in the filter, stated plainly: removal operated at cluster-representative resolution (the Foldseek table covers representatives, not members, and is truncated at E <= 10), and 60 of the 1,728 held-out chains had no SIFTS mapping and so never entered the avoid set.

Intended use and limitations

Intended for research in protein design: assigning sequences to generated backbones, redesigning existing scaffolds, and exploring sequence diversity compatible with a fold.

It does not predict whether a designed protein will express, fold efficiently, remain soluble, or retain function. Structural self-consistency is a necessary but not sufficient criterion.

Practical guidance:

• Filter by refolding. Fold designs with ESMFold or AlphaFold and compare to the input backbone. This is the most informative check available before ordering.
• Test a panel, not one design. Expect a fraction of designs to work.
• Preserve what matters. Fixing residues you know are functionally important is the most direct way to retain a specific activity.
• Trained primarily on single chains; not a general protein-complex design model.
• Position-wise likelihoods correlate best with stability-like phenotypes and less well with binding or activity. Not a general variant-effect predictor.

Known limitations, specifically

• Residual benchmark overlap is bounded but non-zero. Five CATH test chains (0.45%) have an AFDB training structure closer to them than anything in the CATH training split. Their contribution to mean sequence recovery is bounded at roughly 0.3 percentage points.
• Leakage filtering was at cluster-representative resolution, not per-member, so a member of a retained cluster could in principle be closer to a held-out chain than its representative was.
• Sampling is step-count sensitive when the c_factor is enabled. The default 20 steps over horizon T = 8 gives dt ≈ 0.42, which has not converged for that integration. Results move with step count in that mode; the default path (c_factor off) does not use it.
• Designed sequences are not calibrated probabilities. With the c_factor enabled the terminal simplex state is diffuse by construction — the Dirichlet marginal at K = 21, T = 8 is 0.31 — so per-residue confidences read from the saved state should not be treated as well-calibrated. The argmax sequence is unaffected.
• No sequence-identity deduplication within retained AFDB clusters. Redundancy is controlled at cluster granularity only.

Checkpoint contents

inverse_folddir_model.pt, 38 MB, 9.6M parameters. Training run ablation_387, epoch 1353, selected on the generative-validation metric; that provenance is also recorded inside the file under model_name and epoch.

Distributed for inference. Optimizer state, scheduler state, and RNG state have been stripped, and absolute training paths rewritten. Keys retained:

Key	Purpose
model_state_dict	Model weights
args	Training configuration the sampler reads
graph_builder_params	Graph featurization settings
model_architecture_params	Layer sizes and architecture
epoch, model_name, metrics, timestamp	Provenance

Loaded with weights_only=False, since args contains a configuration object rather than plain tensors.

Citation

The accompanying paper is not out yet. Until it is, cite the software:

@software{inversefolddir,
  title  = {Inverse FoldDir: Flexibility-Aware Structure-Conditioned Protein
            Sequence Design with Dirichlet Flow Matching},
  author = {Tartici, Alp and contributors},
  year   = {2026},
  url    = {https://github.com/AlpTartici/inversefolddir},
  note   = {Software. Model weights:
            https://huggingface.co/AlpTartici/inversefolddir}
}

Acknowledgements

Builds on microsoft/InverseFoldDir (MIT, © Microsoft Corporation), which in turn incorporates gvp-pytorch (Jing et al.) and dirichlet-flow-matching (Stärk et al.).