Binding pocket optimization based on force fields and docking scoring functions
☆40Oct 22, 2026Updated last week
Alternatives and similar repositories for pocketoptimizer
Users that are interested in pocketoptimizer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Analysis and design of protein-protein or protein-peptide interactions based on atlas database.☆16Sep 27, 2022Updated 4 years ago
- Automated construction of protein chimeras and their analysis.☆15Sep 29, 2023Updated 3 years ago
- ☆17Sep 26, 2025Updated last year
- PARCE version 1.0☆12Feb 1, 2021Updated 5 years ago
- Learning Protein-Ligand Properties with Atomic Environment Vectors☆10Apr 19, 2024Updated 2 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Automatic gromacs protocol from preparation to production with ligand parametrization through☆84Apr 6, 2025Updated last year
- BEER - Biophysical Evaluation Engine for Residues☆13Jun 16, 2026Updated 4 months ago
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆18Nov 14, 2023Updated 2 years ago
- ☆30May 24, 2024Updated 2 years ago
- PREVENT: PRotein Engineering by Variational frEe eNergy approximaTion☆13Jul 4, 2024Updated 2 years ago
- ☆46Jan 10, 2024Updated 2 years ago
- A protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cle…☆40Jul 25, 2024Updated 2 years ago
- Pocket to Concavity is a tool for refinement of Protein-Ligand binding site shape from alpha-spheres☆16Oct 2, 2024Updated 2 years ago
- ☆23Dec 11, 2024Updated last year
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Augmenting a training dataset of the generative diffusion model for molecular docking with artificial binding pockets☆10Jul 17, 2026Updated 3 months ago
- Structure-based self-supervised learning enables ultrafast prediction of stability changes upon mutations☆118Apr 15, 2026Updated 6 months ago
- ☆98Nov 25, 2025Updated 11 months ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Mar 7, 2025Updated last year
- development repository for PyInteraph2☆23Jun 18, 2026Updated 4 months ago
- ☆20Sep 14, 2022Updated 4 years ago
- Unlocking Generative Diversity in Co-Folding Models via Training-Free Conditioning Perturbation☆11Oct 14, 2026Updated 2 weeks ago
- Python module for identification of conserved water molecules from molecular dynamics trajectories.☆15Oct 23, 2026Updated last week
- Deep learning framework for protein sequence design from a backbone scaffold that can leverage the molecular context including non-protei…☆50Nov 4, 2025Updated 11 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- SableBind is an open-source framework dedicated to predicting protein-ligand binding affinity☆13Feb 6, 2025Updated last year
- Scoring methods for predicting the DDG upon protein mutation☆18Feb 20, 2023Updated 3 years ago
- Universal framework for physically based computational protein design☆36Oct 20, 2026Updated last week
- ☆95Sep 25, 2024Updated 2 years ago
- Analysis of non-covalent interactions in MD trajectories☆72Jan 3, 2025Updated last year
- Python package to manage protein structures and their annotations☆46Mar 18, 2026Updated 7 months ago
- Fully automated docking pipeline (can be run in distributed environments)☆88Updated this week
- Docking Tool Benchmarking Workflow☆25Jul 17, 2024Updated 2 years ago
- An Interface-Predicting Language Model for Designing Peptide-Guided Protein Degraders☆18Sep 10, 2024Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- FeatureDock is a protein-ligand docking software guided by physicochemical feature-based local environment learning using Transformer☆44Oct 9, 2024Updated 2 years ago
- repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model☆310Dec 23, 2025Updated 10 months ago
- DrugDomain database☆11Sep 16, 2025Updated last year
- SE(3)-equivariant point cloud networks for virtual screening☆24Apr 29, 2023Updated 3 years ago
- A Consensus Docking Plugin for PyMOL☆88Jun 10, 2024Updated 2 years ago
- Clusters protein chains based on CA distance difference☆19Oct 9, 2026Updated 2 weeks ago
- ☆11Sep 2, 2024Updated 2 years ago