ingcoder / dock-prepLinks
Pipeline converting PDB files to docking-ready PDBQT format
☆19Updated 2 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:
- ☆51Updated 3 months ago
- Creating machine learning algorithms from scratch☆18Updated 3 months ago
- ☆65Updated last year
- This repository contains notebooks for the workshop Python for Cheminformatics-Driven Molecular Docking held on May 1, 2025 in collaborat…☆81Updated last month
- Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range☆33Updated last week
- Open-source tool to generate 3D-ready small molecules for virtual screening☆58Updated this week
- binding free energy estimator 2☆121Updated last month
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆140Updated 3 weeks ago
- BitBIRCH clustering algorithm☆89Updated last month
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆77Updated 2 years ago
- Thompson Sampling☆69Updated 2 months ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 2 months ago
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆48Updated 2 months ago
- The public versio☆59Updated 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
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆67Updated 6 months ago
- Simple protein-ligand complex simulation with OpenMM☆85Updated last year
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆66Updated last year
- Python package to run molecular dynamics simulation of a protein-ligand complex in a single line of code.☆143Updated 2 weeks ago
- Implementations of different GNNs from scratch for chemists☆138Updated last month
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆151Updated last week
- The Free Energy Landscape Analysis tool offers a comprehensive suite for analyzing and visualizing the free energy landscape derived from…☆21Updated 5 months ago
- Pocket dynamics analysis tool☆15Updated 2 months ago
- ☆81Updated 10 months ago
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆19Updated last year
- ☆76Updated 3 years ago
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆125Updated 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
- AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted lig…☆45Updated this week
- Benchmark set for relative free energy calculations.☆110Updated last year