A python package and collection of scripts for computing protein surface meshes, chemical, electrostatic, geometric features, and building/training graph neural network models of protein-nucleic acid binding
☆27Jul 15, 2025Updated 10 months ago
Alternatives and similar repositories for pnabind
Users that are interested in pnabind are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆15May 29, 2024Updated last year
- ML-optimized library design with improved fitness and diversity for protein engineering☆37Nov 5, 2025Updated 6 months ago
- An open-source platform for developing protein models beyond AlphaFold.☆12Jul 15, 2025Updated 10 months ago
- Workshops on Computational Biology organized by our lab☆10Mar 25, 2024Updated 2 years ago
- Repo contains source code of the SurfaceID paper☆28Mar 13, 2024Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- AlphaFold version that is extended to integrate diversity parameters for massive sampling.☆17May 4, 2026Updated 3 weeks ago
- Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer, NeurIPS2024☆28May 27, 2025Updated 11 months ago
- ☆31Dec 12, 2024Updated last year
- Segmentation of nucleic acid binding interface on protein surface with geometric deep learning☆14May 3, 2023Updated 3 years ago
- Local homology search powered by ESM-2 language model, foldseek, hhsuite, and hmmer.☆18Jan 14, 2025Updated last year
- ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models☆39Nov 25, 2024Updated last year
- ☆28Aug 8, 2025Updated 9 months ago
- Google Colab notebooks for running molecular dynamics simulations with GROMACS☆47Oct 6, 2023Updated 2 years ago
- ☆52Jan 10, 2025Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Metal and Water prediction☆14Feb 5, 2025Updated last year
- Some Rosetta Scripts that allow for various simple tasks☆15Jan 27, 2020Updated 6 years ago
- PyDock Tutorial☆36Jul 2, 2018Updated 7 years ago
- CATH: high-throughput protein structure/function annotations☆12Dec 17, 2019Updated 6 years ago
- GraphSite: protein-DNA binding site prediction using graph transformer and predicted protein structures☆62Aug 3, 2024Updated last year
- ☆24May 19, 2025Updated last year
- Novel estimator for the change in stability upon point mutation in monomeric and multimeric proteins.☆64May 21, 2025Updated last year
- ☆16Mar 28, 2025Updated last year
- CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes☆47Jun 17, 2025Updated 11 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13May 12, 2026Updated 2 weeks ago
- test☆14Nov 13, 2020Updated 5 years ago
- Utility scripts to generate and evaluate parametrically guided beta barrel protein backbone structures.☆14Nov 14, 2025Updated 6 months ago
- Predicting Nanobody Binding Epitopes Based on a Pretrained RoBERTa-based Model☆16Jun 4, 2024Updated last year
- ☆21Oct 31, 2024Updated last year
- Kinome-wide structural pocket similarity☆10Dec 26, 2022Updated 3 years ago
- Geometric deep learning of protein–DNA binding specificity☆78Mar 19, 2025Updated last year
- ☆65Sep 14, 2023Updated 2 years ago
- E(3) equivariant graph neural network for PPI site prediction☆11Sep 18, 2023Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆59Jul 22, 2025Updated 10 months ago
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆14Feb 20, 2023Updated 3 years ago
- A method to predict DNA shape features considering farther flanking region.☆40Sep 25, 2024Updated last year
- ☆59May 13, 2026Updated last week
- ☆149Jul 16, 2025Updated 10 months ago
- Fast and accurate protein domain segmentation using Invariant Point Attention☆46May 22, 2025Updated last year
- Implementation of NeurIPS24 paper "Generalized Protein Pocket Generation with Prior-Informed Flow Matching"☆21May 15, 2025Updated last year