mqcomplab / PRIMELinks
protein structure prediction with precision
☆18Updated last year
Alternatives and similar repositories for PRIME
Users that are interested in PRIME are comparing it to the libraries listed below
Sorting:
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- 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
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- ☆65Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆37Updated 11 months ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆66Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆69Updated 6 months ago
- ☆48Updated 2 months ago
- Computational Chemistry Workflows☆53Updated 2 years ago
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆18Updated 9 months ago
- The public versio☆59Updated 2 years ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 2 months ago
- Cryptic pocket prediction using AlphaFold 2☆23Updated 2 years ago
- 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
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆71Updated 5 months 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.☆14Updated last year
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- ☆34Updated last year
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆48Updated 2 months ago
- A tutorials suite for BioSimSpace.☆25Updated 2 months ago
- ☆14Updated 7 months ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆44Updated 4 years ago
- MDANCE is a flexible n-ary clustering package for all applications.☆68Updated last week
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆18Updated 2 months ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 2 years ago
- Fully automated high-throughput MD pipeline☆61Updated 3 weeks ago
- Pocket dynamics analysis tool☆15Updated 2 months ago