Histidine Protonation State Optimizer for setting up MD simulations based on semi-empirical QM resonance
☆20Mar 6, 2026Updated 6 months ago
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☆14Sep 4, 2026Updated 2 weeks ago
- EnsembleFlex - Flexibility Analysis of Structure Ensembles☆20Sep 10, 2025Updated last year
- Ready-To-Use Pymol Plugin for Docking and Minimization☆12Nov 15, 2025Updated 10 months ago
- Alexandria Chemistry Toolkit☆18Updated this week
- ☆25May 8, 2026Updated 4 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A PyMOL plugin with accompanying Docker image for kinase inhibitor binding and affinity prediction☆12Jun 3, 2024Updated 2 years ago
- The LoCoHD metric for protein-protein structure comparison☆15Oct 1, 2025Updated 11 months ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆176Sep 7, 2026Updated 2 weeks ago
- moldrug (AKA mouse) is a Python package for drug-oriented optimization on the chemical space ☆42Updated this week
- ☆47Jan 8, 2026Updated 8 months ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆34Jun 9, 2026Updated 3 months ago
- MM-PBSA method for GROMACS. For full description, please visit homepage:☆15Aug 1, 2026Updated last month
- Cloud-based molecular docking for everyone☆12Jul 1, 2024Updated 2 years ago
- ☆15Jan 31, 2026Updated 7 months 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.
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆26Dec 24, 2025Updated 9 months ago
- ☆15Jan 27, 2025Updated last year
- A package to create, visualize, and analysis PDB-derived pseudo-ensembles.☆12Jan 7, 2026Updated 8 months ago
- A flow matching model for generating conformational ensembles of protein backbones.☆52May 22, 2026Updated 4 months ago
- ⛓️ Boltz with restraint-guided inference☆21Updated this week
- PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.☆153Feb 12, 2025Updated last year
- Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar stru…☆30May 15, 2026Updated 4 months ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆129Jul 28, 2026Updated last month
- A Nextflow pipeline that creates reliable, structure-informed MSAs of thousands of protein sequences which can supplement structural info…☆11Jul 14, 2026Updated 2 months 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.
- An interactive web-based UI app for REINVENT that enables users to generate input files for running REINVENT calculations.☆21Jun 12, 2025Updated last year
- P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching☆46May 22, 2025Updated last year
- PREVENT: PRotein Engineering by Variational frEe eNergy approximaTion☆13Jul 4, 2024Updated 2 years ago
- Generate Simple Pharmacophore Models with RDKit☆51Updated this week
- Cheminformatic extension for SQLAlchemy☆18Aug 9, 2026Updated last month
- ☆52Jun 15, 2026Updated 3 months ago
- A simple app to generate a predictive ML model from any ChEMBL target via UniprotID☆18Apr 24, 2026Updated 5 months ago
- Megalodon☆24Jul 22, 2025Updated last year
- Explicit crosslinks in AlphaFold 3☆22Mar 17, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A Rust library for parsing PDB (Protein Data Bank) files☆21Sep 16, 2026Updated last week
- Fast protein backbone flexibility prediction model☆41Sep 9, 2026Updated 2 weeks ago
- 💊 Cutting-edge automation of computational drug discovery pipelines☆38Jun 14, 2026Updated 3 months ago
- design by evolutionary algorithm☆23Aug 23, 2026Updated last month
- Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations☆22Feb 25, 2026Updated 6 months ago
- Sidechain conditioning and modeling for full-atom protein sequence design☆150Nov 11, 2025Updated 10 months ago
- ☆18Aug 28, 2025Updated last year