BILAB / pdb2oniomLinks
A python implementation of pdb2oniom for QM/MM (ONIOM) calculations
☆10Updated 2 weeks ago
Alternatives and similar repositories for pdb2oniom
Users that are interested in pdb2oniom are comparing it to the libraries listed below
Sorting:
- Free Parametrization for Small Molecules☆45Updated last week
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- ☆16Updated last month
- Weighted Ensemble Data Analysis and Plotting☆24Updated 4 months ago
- Analysis of non-covalent interactions in MD trajectories☆63Updated 9 months ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆31Updated last month
- Fully automated high-throughput MD pipeline☆80Updated last month
- MDPath - A tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral ang…☆21Updated 2 weeks ago
- A tutorials suite for BioSimSpace.☆28Updated last week
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆17Updated 4 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- ☆18Updated 3 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆32Updated last month
- ☆30Updated 2 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆18Updated 2 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 6 years ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆20Updated 5 months ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 2 months ago
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆19Updated last year
- 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
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆71Updated 2 weeks ago
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆14Updated 4 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆30Updated last month
- ☆39Updated last year
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆13Updated 6 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated last year
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Updated 2 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…☆16Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 2 weeks ago