limresgrp / FMAP_v1Links
Codes to use funnel-metadynamics and funnel metadynamics automated protocol
☆30Updated 3 years ago
Alternatives and similar repositories for FMAP_v1
Users that are interested in FMAP_v1 are comparing it to the libraries listed below
Sorting:
- ☆25Updated 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.☆50Updated 5 months ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆11Updated 3 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- 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 package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated last month
- Random Acceleration Molecular Dynamics in GROMACS☆39Updated last year
- ☆67Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years 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
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆19Updated 3 months ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 3 years ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆70Updated 7 months ago
- A tutorials suite for BioSimSpace.☆25Updated 3 months ago
- Computational Chemistry Workflows☆54Updated 3 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆66Updated 2 years 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 2 months ago
- ☆39Updated last year
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆83Updated last month
- ☆14Updated 8 months ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Updated 4 years ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 3 months ago
- An open library to work with pharmacophores.☆45Updated 2 years ago
- Dynamic pharmacophore modeling of molecular interactions☆35Updated last year
- ☆28Updated 3 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year