ingcoder / dock-prepLinks
Pipeline converting PDB files to docking-ready PDBQT format
☆21Updated 4 months ago
Alternatives and similar repositories for dock-prep
Users that are interested in dock-prep are comparing it to the libraries listed below
Sorting:
- ☆67Updated 2 years ago
- ☆54Updated 5 months ago
- Ready-To-Use Pymol Plugin for Docking and Minimization☆11Updated 2 months ago
- Open-source tool to generate 3D-ready small molecules for virtual screening☆63Updated last month
- Creating machine learning algorithms from scratch☆18Updated 5 months ago
- Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range☆43Updated last month
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆57Updated 4 months ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆70Updated 8 months ago
- binding free energy estimator 2☆126Updated last week
- BitBIRCH clustering algorithm☆92Updated last month
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 4 months ago
- This repository contains notebooks for the workshop Python for Cheminformatics-Driven Molecular Docking held on May 1, 2025 in collaborat…☆83Updated 3 months ago
- The Free Energy Landscape Analysis tool offers a comprehensive suite for analyzing and visualizing the free energy landscape derived from…☆23Updated 7 months ago
- The public versio☆62Updated 2 years ago
- ☆85Updated last year
- Thompson Sampling☆74Updated 4 months ago
- 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
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆53Updated 4 months ago
- Python package to run molecular dynamics simulation of a protein-ligand complex in a single line of code.☆164Updated last month
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆67Updated 2 years ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆146Updated this week
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆79Updated 2 years ago
- Implementations of different GNNs from scratch for chemists☆147Updated 2 weeks ago
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆26Updated 2 months ago
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆19Updated last year
- Simple protein-ligand complex simulation with OpenMM☆87Updated 2 years ago
- Benchmark set for relative free energy calculations.☆113Updated last year
- ☆77Updated 3 years ago
- ☆51Updated 2 months ago
- rdkit scripts making life easier☆70Updated 2 weeks ago