Histidine Protonation State Optimizer for setting up MD simulations based on semi-empirical QM resonance
☆20Mar 6, 2026Updated 7 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:
- ☆14Mar 15, 2025Updated last year
- ☆13May 26, 2022Updated 4 years ago
- 2D Protein-Ligand Interaction Generator with PLIP output☆10Sep 7, 2025Updated last year
- Constava analyzes conformational ensembles calculating conformational state propensities and conformational state variability.☆11Mar 16, 2026Updated 7 months ago
- ☆13Jul 11, 2026Updated 3 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.
- Structure prediction of alternative protein conformations☆86Feb 24, 2025Updated last year
- ☆11Mar 27, 2026Updated 7 months ago
- Distribution package for BaNDyT: Bayesian Network Analysis of Dynamic Trajectories☆11Mar 30, 2026Updated 7 months ago
- Pharmacon: A Molecular Dynamics Analysis Toolkit☆25Oct 5, 2026Updated 3 weeks ago
- A PyMOL plugin with accompanying Docker image for kinase inhibitor binding and affinity prediction☆12Jun 3, 2024Updated 2 years ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆66Dec 17, 2025Updated 10 months ago
- PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.☆152Feb 12, 2025Updated last year
- Cyclic peptide binder design using a fragment docking and assembling strategy☆12May 20, 2025Updated last year
- EnsembleFlex - Flexibility Analysis of Structure Ensembles☆20Sep 10, 2025Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Automated Adaptive Absolute alchemical Free Energy calculator☆134Oct 5, 2026Updated 3 weeks ago
- Rapid construction of chemical pipelines in interactive notebooks and cli usage☆14Updated this week
- Protein design and sculpting using Rosetta and Deep learning methods (RFDiff and Alphafold2)☆75Oct 22, 2026Updated last week
- PyTorch Implementation of CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference☆11May 29, 2024Updated 2 years ago
- ☆52Jun 15, 2026Updated 4 months ago
- A simple tool for creating and running MD simulations, using Jupyter and OpenMM☆12Aug 8, 2025Updated last year
- ☆40Jun 10, 2025Updated last year
- design by evolutionary algorithm☆23Oct 20, 2026Updated 2 weeks ago
- ⛓️ Boltz with restraint-guided inference☆22Sep 28, 2026Updated last month
- 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.
- Preprocessing file generator (v1) and hosted Boltz-2 API builder/submitter (v2.0): binary, ternary, or N-body protein-ligand-DNA-RNA bind…☆12Oct 22, 2026Updated last week
- ☆48Jan 8, 2026Updated 9 months ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆179Oct 26, 2026Updated last week
- a python package to analyze short molecular dynamics simulations for the effect of point mutations on stability☆14Aug 18, 2026Updated 2 months ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 6 years ago
- Ready-To-Use Pymol Plugin for Docking and Minimization☆11Nov 15, 2025Updated 11 months ago
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆26Dec 24, 2025Updated 10 months ago
- An interactive web-based UI app for REINVENT that enables users to generate input files for running REINVENT calculations.☆20Jun 12, 2025Updated last year
- MDDG is a lightweight Python code that allows MD trajectories to be visualised in terms of disconnectivity graphs.☆12Jul 23, 2026Updated 3 months ago
- 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.
- ☆12Jun 29, 2025Updated last year
- ☆68Apr 28, 2025Updated last year
- Fast protein backbone flexibility prediction model☆42Sep 9, 2026Updated last month
- Alexandria Chemistry Toolkit☆18Oct 27, 2026Updated last week
- FeNNol Pretrained Models Collection☆22Dec 17, 2025Updated 10 months ago
- Sire Molecular Simulations Framework☆69Updated this week
- Data sharing for High-throughput Prediction of Changes in Protein Conformational Distributions with Subsampled AlphaFold2☆44May 15, 2024Updated 2 years ago