BILAB / pdb2oniom
A python implementation of pdb2oniom for QM/MM (ONIOM) calculations
☆10Updated 8 months ago
Alternatives and similar repositories for pdb2oniom:
Users that are interested in pdb2oniom are comparing it to the libraries listed below
- Weighted Ensemble Data Analysis and Plotting☆22Updated 4 months ago
- Tools to build coarse grained models and perform simulations with OpenMM☆20Updated 2 years ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆16Updated 2 months ago
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆12Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆12Updated 5 years ago
- ☆27Updated last year
- ☆18Updated 3 years ago
- Multiscale Simulation Tool for Backmapping☆16Updated this week
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆21Updated 5 years ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆15Updated 6 months ago
- ☆13Updated this week
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆23Updated 7 months ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆17Updated this week
- Cloud-based Drug Binding Structure Prediction☆34Updated 4 months ago
- A tutorials suite for BioSimSpace.☆20Updated last month
- ☆25Updated last year
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆16Updated 6 months ago
- ☆12Updated last year
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆20Updated last week
- Automate MD associated calculations☆54Updated 2 weeks ago
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆21Updated this week
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆11Updated 8 months ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆14Updated last year
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆17Updated 4 years ago
- ☆13Updated last month
- Entropy from PDB conformational ensembles☆7Updated 9 months ago
- A collections of scripts for working molecular dynamics simulations☆41Updated 7 months ago
- ☆33Updated 4 months ago
- Python module for identification of conserved water molecules from molecular dynamics trajectories.☆12Updated last month