Martini-Force-Field-Initiative / OLIVESLinks
Algorithm for identifying hydrogen bond networks in CG proteins to implement Go-like Martini 3 models
☆13Updated 11 months ago
Alternatives and similar repositories for OLIVES
Users that are interested in OLIVES are comparing it to the libraries listed below
Sorting:
- ☆28Updated 4 months ago
- ☆28Updated last year
- Computational Chemistry Workflows☆55Updated 3 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆30Updated 2 weeks ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆26Updated 2 years ago
- ☆25Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 3 weeks ago
- Weighted Ensemble Data Analysis and Plotting☆24Updated 3 months ago
- A tutorials suite for BioSimSpace.☆26Updated 4 months ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- ☆18Updated 3 years ago
- Software tools for fragment-based drug discovery (FBDD)☆27Updated 5 years ago
- ☆35Updated 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.☆51Updated 6 months ago
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆12Updated 5 months ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Updated last year
- A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening☆30Updated 4 months ago
- MolTaut, a tool for the rapid generation of favorable states of drug-like molecules in water☆18Updated 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
- 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 3 months ago
- Analysis of non-covalent interactions in MD trajectories☆63Updated 8 months ago
- ☆21Updated 9 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Updated 9 months ago
- 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
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago