Python module for identification of conserved water molecules from molecular dynamics trajectories.
☆14Mar 13, 2026Updated last week
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☆18Mar 13, 2026Updated last week
- Multiscale Simulation Tool for Backmapping☆22Mar 13, 2026Updated last week
- Python code to run Supervised Molecular Dynamics (SuMD) simulations☆16Apr 24, 2024Updated last year
- Collection of tools to help initialize and manipulate geometries in two and three dimensions.☆24Mar 12, 2026Updated last week
- Row is a command line tool that helps you manage workflows on HPC resources.☆16Updated this week
- ☆12Feb 26, 2026Updated 3 weeks ago
- ☆14Jun 4, 2024Updated last year
- Tool suite for analysing molecular dynamics trajectories using network analysis and PRS☆53May 30, 2025Updated 9 months ago
- Molecular simulation toolkit☆20Sep 17, 2025Updated 6 months ago
- Denoising diffusion probabilistic models for replica exchange☆25Feb 19, 2022Updated 4 years ago
- Supporting material for the paper "Data driven collective variables for enhanced sampling"☆20Jun 6, 2024Updated last year
- Corrections to the text of the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford Un…☆32Mar 21, 2023Updated 3 years ago
- Collection of scripts that integrates docking, virtual screening, similarity and molecular modeling programs.☆30Mar 4, 2026Updated 2 weeks ago
- Molecular Dynamics Simulation of Alanine Dipeptide and Dihedral Angle Analysis☆19Jan 2, 2024Updated 2 years ago
- Online solubility prediction tool (streamlit) that runs the top-performing ML model (AqSolPred).☆10Nov 11, 2024Updated last year
- Tool to predict water molecules placement and energy in ligand binding sites☆35Sep 16, 2025Updated 6 months ago
- Tools to build coarse grained models and perform simulations with OpenMM☆25Dec 16, 2022Updated 3 years ago
- App for serotonergic targets☆12Jan 8, 2026Updated 2 months ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆30Oct 22, 2025Updated 4 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Jan 16, 2015Updated 11 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- pymol implementation of WaterDock with Akshay Sridhar (@akshay-sridhar) and refactoring work by Patrick McCubbin (@mccubbinp)☆11Mar 25, 2024Updated last year
- Public version for DistPepFold☆10Jul 17, 2025Updated 8 months ago
- ☆14May 22, 2025Updated 9 months ago
- Efficient Sampling of PROTAC-Induced Ternary Complexes☆12Jun 3, 2025Updated 9 months ago
- Data files which may be used to test examples accompanying the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. T…☆15Oct 7, 2017Updated 8 years ago
- "Independent Component Analysis of BIg Omics Data"☆13Nov 3, 2022Updated 3 years ago
- PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Comp…☆16Oct 23, 2025Updated 4 months ago
- Pocket to Concavity is a tool for refinement of Protein-Ligand binding site shape from alpha-spheres☆16Oct 2, 2024Updated last year
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆18Jun 30, 2025Updated 8 months ago
- Knowledge management for crypto natives.☆18Feb 10, 2026Updated last month
- ☆17Sep 14, 2022Updated 3 years ago
- Computational Chemistry Workflows☆56Jul 19, 2022Updated 3 years ago
- Temperature generator for Replica Exchange MD simulations☆29Dec 14, 2022Updated 3 years ago
- Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest☆14Mar 22, 2023Updated 2 years ago
- Material for the 3rd i-CoMSE Workshop: Methods for Advanced Sampling☆42May 1, 2023Updated 2 years ago
- Accelerated sampling framework with autoencoder-based method☆23Sep 7, 2019Updated 6 years ago
- A cyclic peptide-protein complex dataset derived from AFDB.☆38Updated this week
- OpenMM plugin that implements (an)isotropic polarizable point dipoles and multipoles up to octopoles.☆11Feb 7, 2025Updated last year