JecaTosovic / WaterNetworkAnalysisLinks
Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
☆18Updated last month
Alternatives and similar repositories for WaterNetworkAnalysis
Users that are interested in WaterNetworkAnalysis are comparing it to the libraries listed below
Sorting:
- A tutorials suite for BioSimSpace.☆30Updated 3 weeks ago
- ☆25Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated last year
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- 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
- Python module for identification of conserved water molecules from molecular dynamics trajectories.☆14Updated last month
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- Free Parametrization for Small Molecules☆48Updated last month
- Tool to predict water molecules placement and energy in ligand binding sites☆33Updated 2 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 5 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆57Updated 7 months ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Updated 8 months ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆18Updated 2 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆38Updated 2 years ago
- ☆32Updated 3 months ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆20Updated 6 months ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- Computational Chemistry Workflows☆56Updated 3 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆18Updated last year
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆33Updated 2 months ago
- MDPath - A tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral ang…☆26Updated last week
- protein structure prediction with precision☆26Updated last year
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆42Updated 3 weeks ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 7 months ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago