JecaTosovic / ConservedWaterSearchLinks
Python module for identification of conserved water molecules from molecular dynamics trajectories.
☆12Updated 6 months ago
Alternatives and similar repositories for ConservedWaterSearch
Users that are interested in ConservedWaterSearch are comparing it to the libraries listed below
Sorting:
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 7 months ago
- Multiscale Simulation Tool for Backmapping☆17Updated 2 months ago
- A tutorials suite for BioSimSpace.☆25Updated last month
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆12Updated 2 months ago
- A middleware python tool for computational drug discovery on HPC architectures☆9Updated last year
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆18Updated 2 years ago
- ☆25Updated last year
- Weighted Ensemble Data Analysis and Plotting☆24Updated 8 months ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆13Updated last year
- 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 2 months ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆12Updated 6 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- ☆28Updated 3 weeks ago
- Different run and analysis scripts as described in the research guides.☆13Updated 2 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆16Updated 2 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 2 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆16Updated 9 months ago
- ☆17Updated last year
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆12Updated 2 years ago
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆25Updated last week
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 2 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆29Updated 3 years ago