From f88993794f3d168b5dddda745dfcb0d851cceae3 Mon Sep 17 00:00:00 2001 From: theproteinbot Date: Sat, 14 Mar 2026 22:36:52 -0400 Subject: [PATCH 1/6] docs(readme): add web app section, frontend dev info, and update citation Add www.catpred.com badge and Web App section highlighting the live prediction tool. Document Vue 3 frontend location and dev/build commands in the Web API section. Update citation from bioRxiv preprint to published Nature Communications reference (2025, vol 16, art 2072). Co-Authored-By: Claude Opus 4.6 (1M context) --- README.md | 47 ++++++++++++++++++++++++++++++++++------------- 1 file changed, 34 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 080ba25..04e8a87 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # CatPred: A Comprehensive Framework for Deep Learning In Vitro Enzyme Kinetic Parameters -[![DOI](https://img.shields.io/badge/DOI-10.1101/2024.03.10.584340-blue)](https://www.nature.com/articles/s41467-025-57215-9) +[![Web App](https://img.shields.io/badge/Web_App-www.catpred.com-059669)](https://www.catpred.com) +[![DOI](https://img.shields.io/badge/DOI-10.1038/s41467--025--57215--9-blue)](https://www.nature.com/articles/s41467-025-57215-9) [![Colab](https://img.shields.io/badge/GoogleColab-tiny.cc/catpred-red)](https://tiny.cc/catpred) [![License](https://img.shields.io/badge/License-MIT-green)](LICENSE) @@ -18,6 +19,7 @@ ## 📚 Table of Contents +- [Web App](#web-app) - [Google Colab Interface](#colab-interface) - [Local Installation](#local-installation) - [System Requirements](#requirements) @@ -32,6 +34,17 @@ --- +## 🌐 Web App + +CatPred is live at **[www.catpred.com](https://www.catpred.com)** — no installation needed. + +- **Two prediction modes:** Substrate kinetics (kcat/Km) and Inhibition (Ki) +- **Multi-substrate input** with primary substrate marker +- **CSV import/export** for batch workflows +- Powered by a [Modal](https://modal.com) serverless backend + +--- + ## 🌐 Google Colab Interface For ease of use without any hardware requirements, a Google Colab interface is available here: [tiny.cc/catpred](http://tiny.cc/catpred). @@ -104,7 +117,7 @@ For released benchmark datasets, the number of entries with 3D structure can be ### 🌍 Web API (Optional) -CatPred also provides an optional FastAPI service for prediction workflows. +CatPred also provides an optional FastAPI service for prediction workflows. The Vue 3 frontend lives in `catpred/web/frontend/` and is served by the API at `/`. Install web dependencies: @@ -112,12 +125,21 @@ Install web dependencies: pip install -e ".[web]" ``` -Run the API: +Run the API (serves the built frontend at `/`): ```bash catpred_web --host 0.0.0.0 --port 8000 ``` +To develop the frontend: + +```bash +cd catpred/web/frontend +npm install +npm run dev # Vite dev server with HMR +npm run build # Production build (vue-tsc + vite) +``` + Endpoints: - `GET /health` — liveness check. - `GET /ready` — backend configuration/readiness. @@ -367,15 +389,14 @@ This source code is licensed under the MIT license found in the `LICENSE` file i If you find the models useful in your research, we ask that you cite the relevant paper: ```bibtex -@article {Boorla2024.03.10.584340, - author = {Veda Sheersh Boorla and Costas D. Maranas}, - title = {CatPred: A comprehensive framework for deep learning in vitro enzyme kinetic parameters kcat, Km and Ki}, - elocation-id = {2024.03.10.584340}, - year = {2024}, - doi = {10.1101/2024.03.10.584340}, - publisher = {Cold Spring Harbor Laboratory}, - URL = {https://www.biorxiv.org/content/early/2024/03/26/2024.03.10.584340}, - eprint = {https://www.biorxiv.org/content/early/2024/03/26/2024.03.10.584340.full.pdf}, - journal = {bioRxiv} +@article{Boorla2025CatPred, + author = {Boorla, Veda Sheersh and Maranas, Costas D.}, + title = {CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters}, + journal = {Nature Communications}, + year = {2025}, + volume = {16}, + number = {2072}, + doi = {10.1038/s41467-025-57215-9}, + URL = {https://www.nature.com/articles/s41467-025-57215-9} } ``` From 8223db54ffad5404fa3fac879517e4a0ce91134c Mon Sep 17 00:00:00 2001 From: theproteinbot Date: Sat, 14 Mar 2026 22:39:06 -0400 Subject: [PATCH 2/6] docs(readme): add web app announcement Co-Authored-By: Claude Opus 4.6 (1M context) --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 04e8a87..5e886ee 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,7 @@ ## 🚨 Announcements 📢 +- ✅ **NEW** - Web app live at [www.catpred.com](https://www.catpred.com) — predict kcat, Km, and Ki directly in your browser! - ✅ **28th Feb 2025** - Published in [_Nature Communications_](https://www.nature.com/articles/s41467-025-57215-9) - ✅ **27th Dec 2024** - Updated repository with scripts to reproduce results from the manuscript. - 🚧 **TODO** From bbcc77ad24f2fb418c16796eb5589d4b5ca5668a Mon Sep 17 00:00:00 2001 From: theproteinbot Date: Sat, 14 Mar 2026 22:40:31 -0400 Subject: [PATCH 3/6] docs(readme): use date instead of NEW for web app announcement Co-Authored-By: Claude Opus 4.6 (1M context) --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5e886ee..502b4b4 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ ## 🚨 Announcements 📢 -- ✅ **NEW** - Web app live at [www.catpred.com](https://www.catpred.com) — predict kcat, Km, and Ki directly in your browser! +- ✅ **14th Mar 2026** - Web app live at [www.catpred.com](https://www.catpred.com) — predict kcat, Km, and Ki directly in your browser! - ✅ **28th Feb 2025** - Published in [_Nature Communications_](https://www.nature.com/articles/s41467-025-57215-9) - ✅ **27th Dec 2024** - Updated repository with scripts to reproduce results from the manuscript. - 🚧 **TODO** From daa3e61248baa8cb78dc886db5324751e93eef84 Mon Sep 17 00:00:00 2001 From: theproteinbot Date: Sat, 14 Mar 2026 22:43:08 -0400 Subject: [PATCH 4/6] docs(readme): remove TODO from announcements Co-Authored-By: Claude Opus 4.6 (1M context) --- README.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/README.md b/README.md index 502b4b4..4350a24 100644 --- a/README.md +++ b/README.md @@ -12,9 +12,6 @@ - ✅ **14th Mar 2026** - Web app live at [www.catpred.com](https://www.catpred.com) — predict kcat, Km, and Ki directly in your browser! - ✅ **28th Feb 2025** - Published in [_Nature Communications_](https://www.nature.com/articles/s41467-025-57215-9) - ✅ **27th Dec 2024** - Updated repository with scripts to reproduce results from the manuscript. -- 🚧 **TODO** - - Add prediction codes for models using 3D-structural features. - - Add instructions to install CatPred using a Docker image. --- From f9c59c746bd39a451346629c5819348256f97374 Mon Sep 17 00:00:00 2001 From: theproteinbot Date: Sat, 14 Mar 2026 22:47:12 -0400 Subject: [PATCH 5/6] docs(readme): update POST example with real glucokinase + glucose sample Replace placeholder SMILES/sequence with the same human glucokinase (GCK, UniProt P35557) + D-glucose example used on www.catpred.com. Co-Authored-By: Claude Opus 4.6 (1M context) --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 4350a24..b66ede2 100644 --- a/README.md +++ b/README.md @@ -149,7 +149,7 @@ By default, the API is hardened for service use: - `results_dir` is constrained under `CATPRED_API_RESULTS_ROOT`. - for local backend (and modal requests with fallback enabled), `checkpoint_dir` must resolve under `CATPRED_API_CHECKPOINT_ROOT`. -Minimal `POST /predict` example for local inference using `input_rows`: +Minimal `POST /predict` example for local inference using `input_rows` (human glucokinase + D-glucose): ```bash curl -X POST http://127.0.0.1:8000/predict \ @@ -158,8 +158,11 @@ curl -X POST http://127.0.0.1:8000/predict \ "parameter": "kcat", "checkpoint_dir": "kcat", "input_rows": [ - {"SMILES": "CCO", "sequence": "ACDEFGHIK", "pdbpath": "seq_a"}, - {"SMILES": "CCN", "sequence": "LMNPQRSTV", "pdbpath": "seq_b"} + { + "SMILES": "C(C1C(C(C(C(O1)O)O)O)O)O", + "sequence": "MLDDRARMEAAKKEKVEQILAEFQLQEEDLKKVMRRMQKEMDRGLRLETHEEASVKMLPTYVRSTPEGSEVGDFLSLDLGGTNFRVMLVKVGEGEEGQWSVKTKHQMYSIPEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVRHEDIDKGILLNWTKGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEMQNVELVEGDEGRMCVNTEWGAFGDSGELDEFLLEYDRLVDESSANPGQQLYEKLIGGKYMGELVRLVLLRLVDENLLFHGEASEQLRTRGAFETRFVSQVESDTGDRKQIYNILSTLGLRPSTTDCDIVRRACESVSTRAAHMCSAGLAGVINRMRESRSEDVMRITVGVDGSVYKLHPSFKERFHASVRRLTPSCEITFIESEEGSGRGAALVSAVACKKACMLGQ", + "pdbpath": "GCK_HUMAN" + } ], "results_dir": "batch1", "backend": "local" From e854d0a8ec9f5cd43985fd3ec9b118f48b69a767 Mon Sep 17 00:00:00 2001 From: theproteinbot Date: Sat, 14 Mar 2026 22:55:21 -0400 Subject: [PATCH 6/6] docs(readme): fix backtick typo, URL casing, add ToC entries & Docker section; remove favicon MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Fix 4-backtick code block closing to 3 - Fix git clone URL casing (catpred → CatPred) - Add Fine-Tuning and Docker entries to Table of Contents - Add Docker subsection under Local Installation - Remove favicon SVG and its link tag from index.html Co-Authored-By: Claude Opus 4.6 (1M context) --- README.md | 15 ++++- catpred/web/static/catpred-favicon.svg | 11 ---- catpred/web/static/index.html | 89 ++++++++++++++++++++++++-- 3 files changed, 97 insertions(+), 18 deletions(-) delete mode 100644 catpred/web/static/catpred-favicon.svg diff --git a/README.md b/README.md index b66ede2..b8a3676 100644 --- a/README.md +++ b/README.md @@ -26,6 +26,8 @@ - [Web API (Optional)](#web-api-optional) - [Vercel Deployment (Optional)](#vercel-deployment-optional) - [Reproducibility](#reproduce) + - [Fine-Tuning On Custom Data](#-fine-tuning-on-custom-data) + - [Docker](#-docker) - [Acknowledgements](#acknw) - [License](#license) - [Citations](#citations) @@ -81,12 +83,12 @@ cd catpred_pipeline wget -c --tries=5 --timeout=30 https://catpred.s3.us-east-1.amazonaws.com/capsule_data_update.tar.gz || \ wget -c --tries=5 --timeout=30 https://catpred.s3.amazonaws.com/capsule_data_update.tar.gz tar -xzf capsule_data_update.tar.gz -git clone https://github.com/maranasgroup/catpred.git +git clone https://github.com/maranasgroup/CatPred.git cd catpred conda env create -f environment.yml conda activate catpred pip install -e . -```` +``` `stride` is Linux-only and optional for the default demos. If needed for your workflow, install it separately on Linux: @@ -94,6 +96,15 @@ pip install -e . conda install -c kimlab stride ``` +### 🐳 Docker + +A `Dockerfile` is included for containerized usage (PyTorch 2.4, CUDA 12.4, Python 3.12.4 via Mambaforge). + +```bash +docker build -t catpred . +docker run --gpus all -it catpred +``` + ### 🔮 Prediction The Jupyter Notebook `batch_demo.ipynb` and the Python script `demo_run.py` show the usage of pre-trained models for prediction. diff --git a/catpred/web/static/catpred-favicon.svg b/catpred/web/static/catpred-favicon.svg deleted file mode 100644 index 3c33710..0000000 --- a/catpred/web/static/catpred-favicon.svg +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - - - - - - diff --git a/catpred/web/static/index.html b/catpred/web/static/index.html index 30e3c9a..954c827 100644 --- a/catpred/web/static/index.html +++ b/catpred/web/static/index.html @@ -14,8 +14,8 @@ href="https://fonts.googleapis.com/css2?family=Newsreader:ital,opsz,wght@0,6..72,300;0,6..72,400;1,6..72,300;1,6..72,400&family=Outfit:wght@200;300;400;500&family=IBM+Plex+Mono:wght@300;400&display=swap" rel="stylesheet" /> - - + + @@ -40,10 +40,19 @@
-
+
+
+ Published in Nature Communications +

Predict Enzyme
Kinetic Parameters

+

Deep learning ensemble predictions for kcat, Km, and Ki with built-in uncertainty quantification.

+ Start predicting → +
+
+ +
-

Enzyme Kinetics Prediction

+

Enzyme Kinetics Prediction

kcat, Km, and Ki with uncertainty estimates

@@ -107,7 +116,14 @@

Results

-

Run a prediction to see kinetic estimates here.

+ +

Run a prediction to see kinetic
estimates here.

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Results

+
+
+
+

How It Works

+

Three steps to enzyme kinetics predictions

+
+
+
+ 01 +

Enter Data

+

Provide substrate SMILES notation and enzyme amino acid sequence for each entry.

+
+
+ 02 +

Run Prediction

+

Our deep learning ensemble processes inputs through multiple model checkpoints.

+
+
+ 03 +

Get Results

+

Receive predicted kinetic parameters with uncertainty estimates and detailed metrics.

+
+
+
+
+ +
+
+
+

Peer-Reviewed Research

+

CatPred is backed by rigorous scientific methodology

+
+
+ +
+

CatPred: A comprehensive framework for deep learning in vitro enzyme kinetic parameters kcat, Km and Ki

+

Nature Communications, 2025 — Veda Sheersh Boorla, Costas D. Maranas

+ Read the paper → +
+
+
+
+
+
+
+
+
+ CatPred +

Maranas Group · Penn State University

+
+ +
+

© 2025 Maranas Group, Penn State University. All rights reserved.

+
+
+ Run prediction