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:
- 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
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- Software tools for fragment-based drug discovery (FBDD)☆27Updated 5 years ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- ☆25Updated last year
- A tutorials suite for BioSimSpace.☆28Updated last week
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated last year
- Free Parametrization for Small Molecules☆47Updated 2 weeks ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 2 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 6 months ago
- ☆28Updated 5 months ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 3 years ago
- Multiscale Simulation Tool for Backmapping☆19Updated last month
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Updated 10 months ago
- Tautomer ratios in solution☆26Updated 4 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- ☆16Updated 8 years ago
- ☆18Updated 3 years ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 3 weeks ago
- Implementation of Shape and Electrostatic similarity metric in deepFMPO.☆45Updated 3 years ago
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆27Updated last month
- Data set of protein-ligand complexes with reliable experimental structures and affinities☆43Updated 3 weeks ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Computational Chemistry Workflows☆55Updated 3 years ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Updated 7 months 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…☆32Updated 4 months ago