floWneffetS / tutorial_dcTMDLinks
Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.
☆10Updated last year
Alternatives and similar repositories for tutorial_dcTMD
Users that are interested in tutorial_dcTMD are comparing it to the libraries listed below
Sorting:
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆12Updated 2 years ago
- Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations☆30Updated last year
- Tools to calculate descriptors from molecular dynamics and it's application to predict drug resistance.☆16Updated 2 years ago
- ML-based molecular representation models using PyTorch☆15Updated 2 months ago
- OpenSMOG is a Python library for performing molecular dynamics simulations using Structure-Based Models. OpenSMOG uses OpenMM.☆12Updated 2 weeks ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 2 months ago
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆19Updated 6 years ago
- Data set of protein-ligand complexes with reliable experimental structures and affinities☆43Updated 3 weeks ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 7 months ago
- Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by …☆28Updated 2 months ago
- Implementation of Shape and Electrostatic similarity metric in deepFMPO.☆45Updated 3 years ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆23Updated last year
- Free Parametrization for Small Molecules☆47Updated 3 weeks ago
- ☆18Updated 3 years ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Updated 5 years ago
- ☆28Updated 5 months ago
- A Python program for QM/MM Simulations based on the Perturbed Matrix Method☆26Updated 2 years ago
- Computational Chemistry Workflows☆55Updated 3 years ago
- Set of tools to generate a multi-eGO force field to perform molecular dynamics simulations☆14Updated last week
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆32Updated last month
- Software tools for fragment-based drug discovery (FBDD)☆27Updated 5 years ago
- ☆25Updated last year
- ChEMBL Similarity Search☆17Updated 4 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆33Updated last month
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago
- Python library to run structure based model (SBM) simulations using the OpenMM toolkit☆23Updated 3 years ago
- Code to accompany "Practical Cheminformatics With Open Source Software"☆16Updated 3 years ago