BILAB / pdb2oniom
A python implementation of pdb2oniom for QM/MM (ONIOM) calculations
☆10Updated 9 months ago
Alternatives and similar repositories for pdb2oniom:
Users that are interested in pdb2oniom are comparing it to the libraries listed below
- Tools to build coarse grained models and perform simulations with OpenMM☆20Updated 2 years ago
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆13Updated last year
- Weighted Ensemble Data Analysis and Plotting☆23Updated 5 months ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆18Updated 3 weeks 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 3 months ago
- ☆27Updated last year
- ☆25Updated last year
- Fully automated high-throughput MD pipeline☆54Updated this week
- ☆18Updated 3 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆12Updated 4 years ago
- A collections of scripts for working molecular dynamics simulations☆42Updated 8 months ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆22Updated last month
- InteractionDrawer is a JavaScript library for the drawing of highly interactive 2D ligand interaction diagrams.☆18Updated last year
- Collection of Python scripts to setup and run simulations with OpenMM☆15Updated 4 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Multiscale Simulation Tool for Backmapping☆16Updated last month
- Binding pocket optimization based on force fields and docking scoring functions☆30Updated 2 months ago
- ☆12Updated last year
- ☆14Updated this week
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆27Updated this week
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆12Updated 5 years ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆17Updated 3 years ago
- ☆13Updated 2 months ago
- Entropy from PDB conformational ensembles☆7Updated 10 months ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆26Updated 8 months ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆21Updated 5 years ago