choderalab / kinase-metadynamicsLinks
To run metadynamics simulations using openMM (based on Peter Eastman's script)
☆13Updated 6 years ago
Alternatives and similar repositories for kinase-metadynamics
Users that are interested in kinase-metadynamics are comparing it to the libraries listed below
Sorting:
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 2 weeks ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆14Updated last year
- Models trained on the SPICE dataset☆10Updated 2 years ago
- ☆25Updated last year
- Examples of applications of pymbar to various problems in simulation and experiment☆21Updated 10 years ago
- Multiscale Simulation Tool for Backmapping☆17Updated 3 months ago
- A collections of scripts for working molecular dynamics simulations☆43Updated last year
- Bayesian Multistate Bennett Acceptance Ratio Method☆13Updated last month
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆12Updated 3 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Cryptic pocket prediction using AlphaFold 2☆23Updated 2 years ago
- ☆15Updated 8 years ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆31Updated 3 weeks ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆14Updated 2 months ago
- McDock: Simple Monte Carlo docking algorithm in C++☆10Updated 8 years ago
- ☆22Updated last week
- A middleware python tool for computational drug discovery on HPC architectures☆9Updated last year
- Weighted Ensemble Data Analysis and Plotting☆24Updated last week
- Absolute solvation free energy calculations with OpenFF and OpenMM☆22Updated 6 months ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 2 months ago
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆16Updated last year
- Python module for identification of conserved water molecules from molecular dynamics trajectories.☆12Updated 3 weeks ago
- ☆10Updated 5 years ago
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated last year
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆27Updated 6 months ago
- A tutorials suite for BioSimSpace.☆25Updated last month
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆17Updated 2 years ago