BILAB / pdb2oniomLinks
A python implementation of pdb2oniom for QM/MM (ONIOM) calculations
☆10Updated 4 months ago
Alternatives and similar repositories for pdb2oniom
Users that are interested in pdb2oniom are comparing it to the libraries listed below
Sorting:
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆14Updated 7 years ago
- Weighted Ensemble Data Analysis and Plotting☆25Updated last month
- Free Parametrization for Small Molecules☆50Updated this week
- Tools to build coarse grained models and perform simulations with OpenMM☆25Updated 3 years ago
- The official GitHub repository for the Nature Communications paper "Computational Design of Generalist Cyclopropanases with Stereodiverge…☆13Updated 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 5 years ago
- ☆17Updated 5 months ago
- Entropy from PDB conformational ensembles☆13Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Updated 6 years ago
- MDPath - A tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral ang…☆26Updated 2 months ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆18Updated 4 years ago
- Adaptive string method implementation in AmberTools23 and Amber22☆14Updated last year
- ☆18Updated 4 years ago
- A collections of scripts for working molecular dynamics simulations☆45Updated 6 months 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 5 months ago
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆60Updated last week
- A tutorials suite for BioSimSpace.☆34Updated 3 months ago
- scripts to find PBD structures for cancer driver proteins☆31Updated 2 weeks ago
- A python script for PyMol to make protein-ligand interaction images.☆17Updated 10 months ago
- ☆21Updated last year
- Rapid Generation of Rare Event Pathways Using Direction Guided Adaptive Sampling: From Ligand Unbinding to Protein (Un)Folding☆38Updated 2 months ago
- ☆32Updated 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
- ☆24Updated 7 months ago
- ☆25Updated 2 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated this week
- ☆22Updated 10 months ago
- Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations☆20Updated last year