MottaStefano / PathDetect-SOMLinks
A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)
☆10Updated 3 years ago
Alternatives and similar repositories for PathDetect-SOM
Users that are interested in PathDetect-SOM 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 last month
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated 3 weeks ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆53Updated 6 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- ☆67Updated 2 years ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 5 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 4 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
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- ☆25Updated last year
- 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
- ☆28Updated 5 months ago
- A tutorials suite for BioSimSpace.☆27Updated 5 months ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆72Updated 8 months ago
- Screening protocol with AUTODOCK-GPU☆13Updated 2 years ago
- ☆35Updated last year
- Free Parametrization for Small Molecules☆36Updated last week
- Random Acceleration Molecular Dynamics in GROMACS☆39Updated last year
- Computational Chemistry Workflows☆55Updated 3 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Updated 7 months ago
- protein structure prediction with precision☆26Updated last year
- Python code for generating Boresch restraints from MD simulations☆22Updated 3 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆71Updated 8 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆16Updated last year
- Fully automated high-throughput MD pipeline☆76Updated last month