williamdlees / AmberUtilsLinks
Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods
☆19Updated 5 years ago
Alternatives and similar repositories for AmberUtils
Users that are interested in AmberUtils are comparing it to the libraries listed below
Sorting:
- Analysis of non-covalent interactions in MD trajectories☆63Updated 9 months ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago
- Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by …☆28Updated 2 months ago
- ☆18Updated 3 years ago
- Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over pop…☆61Updated last month
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆31Updated last month
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆21Updated 4 years ago
- ☆30Updated 2 years ago
- pKa estimates for proteins using an ensemble approach☆29Updated 3 months ago
- MMTSB Tool Set☆32Updated 2 months ago
- Computational Chemistry Workflows☆55Updated 3 years ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 2 months ago
- Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file☆35Updated 3 months ago
- PyRod - Tracing water molecules in molecular dynamics simulations☆51Updated 4 years ago
- ☆25Updated last year
- Software tools for fragment-based drug discovery (FBDD)☆27Updated 5 years ago
- Code to accompany "Practical Cheminformatics With Open Source Software"☆16Updated 3 years ago
- ☆28Updated 5 months ago
- ML-based molecular representation models using PyTorch☆15Updated 2 months ago
- RF-Score-VS binary☆31Updated 6 years ago
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆36Updated last week
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- MD pharmacophores and virtual screening☆33Updated last year
- Python script that creates 2D protein-ligand interaction images☆14Updated 7 years ago
- Tautomer ratios in solution☆26Updated 4 years ago
- Parallelized Open Babel & Autodock suite Pipeline☆24Updated 7 years ago
- Tool suite for analysing molecular dynamics trajectories using network analysis and PRS☆51Updated 5 months ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago