Histidine Protonation State Optimizer for setting up MD simulations based on semi-empirical QM resonance
☆20Mar 6, 2026Updated last month
Alternatives and similar repositories for protonation-optimizer
Users that are interested in protonation-optimizer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Rapid construction of chemical pipelines in interactive notebooks and cli usage☆13Sep 27, 2024Updated last year
- Ready-To-Use Pymol Plugin for Docking and Minimization☆12Nov 15, 2025Updated 5 months ago
- Fast protein backbone flexibility prediction model☆35Jan 4, 2026Updated 3 months ago
- Alexandria Chemistry Toolkit☆16Updated this week
- Free Parametrization for Small Molecules☆52Feb 18, 2026Updated last month
- 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.
- ☆15Jan 31, 2026Updated 2 months ago
- Tools for molecular Docking☆27Jul 24, 2025Updated 8 months ago
- A PyMOL plugin with accompanying Docker image for kinase inhibitor binding and affinity prediction☆12Jun 3, 2024Updated last year
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆166Apr 8, 2026Updated last week
- moldrug (AKA mouse) is a Python package for drug-oriented optimization on the chemical space ☆39Mar 30, 2026Updated 2 weeks ago
- The LoCoHD metric for protein-protein structure comparison☆15Oct 1, 2025Updated 6 months ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆31Apr 4, 2026Updated last week
- Sidechain conditioning and modeling for full-atom protein sequence design☆138Nov 11, 2025Updated 5 months ago
- Cloud-based molecular docking for everyone☆12Jul 1, 2024Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆25Dec 24, 2025Updated 3 months ago
- A package to create, visualize, and analysis PDB-derived pseudo-ensembles.☆10Jan 7, 2026Updated 3 months ago
- PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.☆149Feb 12, 2025Updated last year
- Antibody structure prediction☆37Dec 16, 2025Updated 3 months ago
- An automated enhanced sampling generation of training sets for chemically reactive machine learning interatomic potentials☆22Feb 13, 2026Updated 2 months ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆115Feb 9, 2026Updated 2 months ago
- PyTorch Implementation of CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference☆11May 29, 2024Updated last year
- MolModa provides a secure, accessible environment where users can perform molecular docking entirely in their web browsers.☆20Apr 5, 2026Updated last week
- A toolkit developed to predict and analyze PROTAC-mediated ternary complexes using AlphaFold3 and Boltz-1.☆41Jul 17, 2025Updated 8 months ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Google Colaboratory Notebooks for Computational Biochemistry☆21Jun 15, 2025Updated 10 months ago
- P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching☆43May 22, 2025Updated 10 months ago
- Flexibility-conditioned protein structure design☆33Mar 10, 2026Updated last month
- PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.☆239Nov 5, 2025Updated 5 months ago
- Public version for Distance-AF☆31Aug 17, 2025Updated 7 months ago
- Explicit crosslinks in AlphaFold 3☆23Mar 17, 2025Updated last year
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆76Mar 18, 2026Updated 3 weeks ago
- The public versio☆89Jun 26, 2023Updated 2 years ago
- ☆28Feb 27, 2026Updated last month
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Molecular Dynamics on Google Compute Engine, Colab, AWS (Amazon Web Services) and other Cloud Computing services☆24Oct 18, 2025Updated 5 months ago
- ☆18Aug 28, 2025Updated 7 months ago
- Protein representation and design under a single training scheme☆24Mar 3, 2026Updated last month
- Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations☆20Feb 25, 2026Updated last month
- Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation☆141Jul 21, 2023Updated 2 years ago
- PREVENT: PRotein Engineering by Variational frEe eNergy approximaTion☆13Jul 4, 2024Updated last year
- Deep generative modeling of protein structural ensembles☆37Sep 22, 2025Updated 6 months ago