JecaTosovic / ConservedWaterSearch
Python module for identification of conserved water molecules from molecular dynamics trajectories.
☆12Updated 5 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 6 months ago
- Multiscale Simulation Tool for Backmapping☆17Updated last month
- Tools to build coarse grained models and perform simulations with OpenMM☆23Updated 2 years ago
- A tutorials suite for BioSimSpace.☆25Updated 2 weeks ago
- ☆25Updated last year
- A middleware python tool for computational drug discovery on HPC architectures☆9Updated last year
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆15Updated 2 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆15Updated 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
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆13Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated 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 last month
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆27Updated 3 years ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆12Updated 2 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆12Updated 6 years ago
- ☆11Updated 11 months ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆12Updated 2 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last month
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- Python code for generating Boresch restraints from MD simulations☆20Updated 2 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆36Updated 9 months ago
- ☆27Updated last week
- A collections of scripts for working molecular dynamics simulations☆43Updated 11 months ago
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆24Updated 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
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 2 years ago
- Automatic CHARMM-GUI browser interaction with Python☆14Updated 2 years ago