huichenggong / Learning-Computation-with-ChenggongLinks
☆39Updated 11 months ago
Alternatives and similar repositories for Learning-Computation-with-Chenggong
Users that are interested in Learning-Computation-with-Chenggong are comparing it to the libraries listed below
Sorting:
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆67Updated 6 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆77Updated 2 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆66Updated last year
- ☆65Updated last year
- ☆20Updated last year
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆57Updated 2 months ago
- ☆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 3 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- binding free energy estimator 2☆120Updated last month
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆83Updated 2 weeks ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 2 months ago
- The public versio☆59Updated 2 years ago
- Pocket dynamics analysis tool☆15Updated 2 months ago
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- Simple protein-ligand complex simulation with OpenMM☆85Updated last year
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆44Updated 4 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆25Updated 2 weeks ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆48Updated 2 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆71Updated 5 months ago
- some scripts for analysis of MD and CADD. And some tutorials.☆57Updated 11 months ago
- Trusted force field files for gromacs☆53Updated 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
- Computational Chemistry Workflows☆53Updated 2 years ago
- Fully automated high-throughput MD pipeline☆61Updated 3 weeks ago
- Open-source tool to generate 3D-ready small molecules for virtual screening☆56Updated this week
- ☆76Updated last year