jaredsagendorf / pnabindView external linksLinks
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 6 months ago
Alternatives and similar repositories for pnabind
Users that are interested in pnabind are comparing it to the libraries listed below
Sorting:
- ☆15May 29, 2024Updated last year
- Google Colab notebooks for running molecular dynamics simulations with GROMACS☆44Oct 6, 2023Updated 2 years ago
- ML-optimized library design with improved fitness and diversity for protein engineering☆36Nov 5, 2025Updated 3 months ago
- Workshops on Computational Biology organized by our lab☆10Mar 25, 2024Updated last year
- Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer, NeurIPS2024☆27May 27, 2025Updated 8 months ago
- Metal and Water prediction☆13Feb 5, 2025Updated last year
- An open-source platform for developing protein models beyond AlphaFold.☆12Jul 15, 2025Updated 6 months ago
- Repo contains source code of the SurfaceID paper☆27Mar 13, 2024Updated last year
- ☆30Dec 12, 2024Updated last year
- Implementation of NeurIPS24 paper "Generalized Protein Pocket Generation with Prior-Informed Flow Matching"☆19May 15, 2025Updated 8 months ago
- DomainMapper is a parser for hmmscan full output files built centrally around ECOD domain definitions. Users can optimize DomainMapper's …☆13Dec 13, 2023Updated 2 years ago
- CATH: high-throughput protein structure/function annotations☆12Dec 17, 2019Updated 6 years ago
- ☆15Mar 28, 2025Updated 10 months ago
- Utility scripts to generate and evaluate parametrically guided beta barrel protein backbone structures.☆14Nov 14, 2025Updated 2 months ago
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13Apr 11, 2025Updated 10 months ago
- Local homology search powered by ESM-2 language model, foldseek, hhsuite, and hmmer.☆17Jan 14, 2025Updated last year
- Segmentation of nucleic acid binding interface on protein surface with geometric deep learning☆14May 3, 2023Updated 2 years ago
- test☆14Nov 13, 2020Updated 5 years ago
- Predicting Nanobody Binding Epitopes Based on a Pretrained RoBERTa-based Model☆15Jun 4, 2024Updated last year
- Novel estimator for the change in stability upon point mutation in monomeric and multimeric proteins.☆61May 21, 2025Updated 8 months ago
- PyDock Tutorial☆35Jul 2, 2018Updated 7 years ago
- GraphSite: protein-DNA binding site prediction using graph transformer and predicted protein structures☆61Aug 3, 2024Updated last year
- Some Rosetta Scripts that allow for various simple tasks☆14Jan 27, 2020Updated 6 years ago
- ☆58Nov 7, 2025Updated 3 months ago
- AlphaFold version that is extended to integrate diversity parameters for massive sampling.☆16Feb 6, 2026Updated last week
- CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes☆40Jun 17, 2025Updated 7 months ago
- ☆27Aug 8, 2025Updated 6 months ago
- ACGCN: Graph Convolutional Networks for Activity Cliff Prediction Between Matched Molecular Pairs (Park et al., 2022)☆20Feb 10, 2023Updated 3 years ago
- ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models☆39Nov 25, 2024Updated last year
- ☆65Sep 14, 2023Updated 2 years ago
- Fast and accurate protein domain segmentation using Invariant Point Attention☆46May 22, 2025Updated 8 months ago
- A domain parser for Alphafold models☆46Dec 12, 2023Updated 2 years ago
- ☆15Jun 21, 2022Updated 3 years ago
- Quantifying the nativeness of antibody sequences using long short-term memory networks☆18Dec 17, 2021Updated 4 years ago
- This is the official code repository for the paper FLOP: Tasks for Fitness Landscapes Of Protein wildtypes by Groth et al.☆22Jun 26, 2023Updated 2 years ago
- ☆55Jul 22, 2025Updated 6 months ago
- ☆21Oct 31, 2024Updated last year
- Material to run the HADDOCK antibody-antigen modelling protocol☆23Feb 3, 2026Updated last week
- A conditionally adapted protein language model for the generation of enzymes☆23Nov 26, 2024Updated last year