miqueleg / protonation-optimizerLinks
Histidine Protonation State Optimizer for setting up MD simulations based on semi-empirical QM resonance
☆15Updated 2 weeks ago
Alternatives and similar repositories for protonation-optimizer
Users that are interested in protonation-optimizer are comparing it to the libraries listed below
Sorting:
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆24Updated last month
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- Weighted Ensemble Data Analysis and Plotting☆24Updated 8 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- Fully automated high-throughput MD pipeline☆60Updated 3 weeks ago
- Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations☆19Updated 8 months ago
- ☆45Updated 3 weeks ago
- ☆12Updated last year
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆29Updated last week
- ☆14Updated 5 months ago
- Computational Chemistry Workflows☆53Updated 2 years ago
- Binding pocket optimization based on force fields and docking scoring functions☆33Updated 2 months ago
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆23Updated 5 months ago
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆18Updated last year
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆16Updated 8 months ago
- Pocket dynamics analysis tool☆13Updated last month
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆17Updated last year
- ☆31Updated 7 months ago
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆12Updated 2 years ago
- A curated list of tools and servers for computer-aided drug design and discovery.☆27Updated 2 weeks ago
- protein structure prediction with precision☆18Updated last year
- ☆28Updated last month
- A python module to plot secondary structure schemes☆25Updated last year
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆37Updated 10 months ago
- Fully automated docking pipeline (can be run in distributed environments)☆44Updated last week
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆63Updated 5 months ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆29Updated 3 months ago
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆47Updated 3 weeks ago