bussilab / MDRefine
☆14Updated this week
Alternatives and similar repositories for MDRefine:
Users that are interested in MDRefine are comparing it to the libraries listed below
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆13Updated last year
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆20Updated last year
- Tools to build coarse grained models and perform simulations with OpenMM☆20Updated 2 years ago
- ☆29Updated last year
- ☆32Updated 5 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
- Multiscale Simulation Tool for Backmapping☆16Updated last month
- ☆25Updated last year
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated 2 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- ☆21Updated 4 months ago
- Weighted Ensemble Data Analysis and Plotting☆23Updated 5 months 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 7 months ago
- A collections of scripts for working molecular dynamics simulations☆42Updated 8 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- Bayesian Multistate Bennett Acceptance Ratio Method☆13Updated last month
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Python code for generating Boresch restraints from MD simulations☆19Updated 2 years ago
- Gromacs Implementation of OPLS-AAM Force field☆13Updated 6 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆36Updated last year
- Temperature generator for Replica Exchange MD simulations☆27Updated 2 years ago
- ☆20Updated 5 months ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆17Updated 4 years ago
- A tutorials suite for BioSimSpace.☆21Updated 2 months ago
- Software for the prediction of DEER and PRE data from conformational ensembles.☆12Updated 5 months 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
- Models trained on the SPICE dataset☆10Updated 2 years ago
- Fully automated docking pipeline (can be run in distributed environments)☆40Updated last week