CAFE

Cofolding-Approach to Fragment Exploration of Allosteric and Cryptic Binding Sites

CAFE is a workflow for probing orthosteric and allosteric pockets with fragment libraries via structure prediction (Boltz) and geometric localization. This repository packages the fragment catalogs, pocket reference structures, and pipeline entry points used in the study.

Private preview release (THGLab).

What is included

Path	Contents
data/fragments/	Paper-style fragment catalogs (kinase, nonkinase, Enamine)
data/references/sites.csv	Orthosteric / allosteric site definitions (PDB, chain, ligand, resseq)
data/references/pdb/	Reference structures used for alignment and localization
scripts/fragmentation/	Build / regenerate fragment libraries (BRICS)
scripts/boltz/	Cofolding: prepare inputs → predict → align
scripts/localization/	Score poses vs orthosteric / allosteric references

A three-arm worked example (no ADP / ADP / Type‑1) is in examples/mapk14_map_a005/.

Quickstart (MAP-A005 · three arms)

From the repo root (needs numpy; RDKit only for the optional BRICS demo):

# Score pre-aligned Boltz poses for each ATP-site condition
for arm in no_adp with_adp type1; do
  PYTHONPATH=scripts python scripts/localization/score_poses.py \
    --target MAPK14 \
    --poses examples/mapk14_map_a005/aligned_poses/$arm \
    --out examples/mapk14_map_a005/localization_${arm}.csv
done

Expected at 5 Å: no ADP → 10/10 ortho; ADP and Type‑1 → 10/10 allo.

Boltz input YAMLs for the same fragment are under examples/mapk14_map_a005/boltz_yamls/. See that folder’s README for rebuild / predict / align steps.

Fragment catalogs

Human-readable IDs for the libraries used in the paper:

File	Count	ID pattern	Notes
kinase_fragment_catalog.csv	232	{KIN}-A### / {KIN}-O###	116 allosteric + 116 orthosteric BRICS fragments across AKT2, CDK2, CHEK1, CSNK2A1, MAPK14
nonkinase_fragment_catalog.csv	37	PTP-A### / KRA-A###	Allosteric-only BRICS fragments for PTP1B (23) and KRAS (14)
enamine_fragment_catalog.csv	300	ENA-###	Enamine diversity set ordered by selection_rank

Kinase abbreviations: AKT, CDK, CHK, CSK, MAP.

Example rows:

CHK-A000  allosteric  CHEK1  3F9N/38M  …
MAP-O012  orthosteric MAPK14 …
PTP-A000  allosteric  PTP1B  1T49/892 …
ENA-000   enamine     Z1473029920 …

Reference structures

Pocket geometry is defined in data/references/sites.csv:

target,role,pdb_id,chain,ligand,resseq
MAPK14,ortho,3S3I,A,CQ0,1
MAPK14,allo,5N63,A,8OW,401
…

PDB files live under:

data/references/pdb/
  kinases/<TARGET>/<PDB>.pdb
  nonkinase/<TARGET>/<PDB>.pdb

Kinases — one orthosteric alignment frame per target, plus allosteric localization references:

Target	Ortho frame	Allo refs
AKT2	2JDO	8Q61, 9C1W
CDK2	2UUE	6Q3F, 6Q49, 6Q4K, 8VQ3, 8VQ4
CHEK1	2YEX	3F9N, 3JVR, 3JVS
CSNK2A1	3WAR	5MMF, 5MOD, 5OSU, 6GIH
MAPK14	3S3I	3NEW, 5N63, 5N64, 5N67, 5N68, 8X3M, 8YD9

Nonkinases

Target	Ortho / blocker	Allo refs
PTP1B	5K9W (OTA)	1T49, 1T4J, 7GSA, 7GTQ, 8G65, 8G68, 8G69
KRAS	4OBE (GDP)	7RPZ, 5V71

Structures are RCSB-derived, cleaned to the chains used in the study. Cite the PDB IDs in any downstream work.

Pipeline overview

fragments ──► Boltz cofolding ──► align to ortho frame ──► localize vs sites.csv
   │                                    │                         │
 catalogs                         predicted poses          % in pocket (e.g. ≤5 Å)

Typical arms for kinases: empty ATP site (no_adp), ADP-occupied, and Type‑1 inhibitor–occupied (verified CCD ligand). Localization uses heavy-atom minimum distance to reference ligands listed in sites.csv.

Script folders are staged for a public-facing API; wire them to your Boltz install and compute environment as needed.

Setup

conda env create -f environment.yml
conda activate cafe

Requires a working Boltz installation for cofolding (GPU recommended). RDKit is used for fragmentation; MDAnalysis or PyMOL can be used for alignment helpers.

Repository layout

CAFE/
├── README.md
├── LICENSE
├── environment.yml
├── data/
│   ├── fragments/
│   └── references/
│       ├── sites.csv
│       └── pdb/
├── examples/
│   └── mapk14_map_a005/         # no ADP / ADP / Type-1 walkthrough
└── scripts/
    ├── lib/                     # shared PDB / sites / Kabsch helpers
    ├── fragmentation/brics_cut.py
    ├── boltz/prepare_yaml.py
    ├── boltz/align_to_ortho.py
    └── localization/score_poses.py

Citation

Manuscript in preparation. Please cite this repository and the RCSB PDB entries for any reference structures you reuse.

Enamine catalog identifiers (Z…) remain the property of Enamine; SMILES are provided for reproducibility of the computational screen.

License

Code is released under the MIT License (see LICENSE). Reference PDB coordinates remain subject to the RCSB PDB terms; fragment catalog SMILES are provided for research use.