A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit
☆75Feb 19, 2026Updated last week
Alternatives and similar repositories for ccdutils
Users that are interested in ccdutils are comparing it to the libraries listed below
Sorting:
- Calculation of interatomic interactions in molecular structures☆120Sep 3, 2024Updated last year
- Python package for handling ModelCIF mmCIF and BinaryCIF files☆13Feb 12, 2026Updated 2 weeks ago
- Data and analysis scripts for understanding molecular entropies, including conformer flexibility☆12Mar 29, 2021Updated 4 years ago
- ☆10Nov 17, 2020Updated 5 years ago
- A thin wrapper around ProteinMPNN for convenient sampling without having to write out or consume files☆12Apr 29, 2024Updated last year
- Fully automated high-throughput MD pipeline☆89Feb 13, 2026Updated 2 weeks ago
- Explain a SMARTS using SmartsView (K. Schomburg and M. Rarey)☆17Oct 4, 2021Updated 4 years ago
- An automated scoring function to facilitate and standardize the evaluation of goal-directed generative models for de novo molecular desig…☆224Jan 20, 2026Updated last month
- ☆24Jun 23, 2021Updated 4 years ago
- PDBFixer fixes problems in PDB files☆626Oct 30, 2025Updated 4 months ago
- ☆37Feb 5, 2024Updated 2 years ago
- DeepCoSI: a Structure-based Deep Graph Learning Network Method for Covalent Binding Site Identification.☆14Oct 22, 2023Updated 2 years ago
- GUIDEMOL: a Python graphical user interface for molecular descriptors based on RDKit☆14Jan 25, 2024Updated 2 years ago
- 📐 Symmetry-corrected RMSD in Python☆111Dec 22, 2025Updated 2 months ago
- Protein Ligand INteraction Dataset and Evaluation Resource☆273Feb 21, 2026Updated last week
- Fully automated docking pipeline (can be run in distributed environments)☆55Feb 21, 2026Updated last week
- BinaryCIF is a data format for storing text based CIF files using a more efficient binary encoding.☆30Oct 14, 2024Updated last year
- DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind.☆38Updated this week
- ☆54Jan 17, 2026Updated last month
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆140Nov 10, 2025Updated 3 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.☆61Dec 17, 2025Updated 2 months ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆72Feb 13, 2026Updated 2 weeks ago
- wwPDB PDBx/mmCIF Dictionary☆10Jan 28, 2026Updated last month
- Implementation of the Paper "iScore: A ML-Based Scoring Function for de novo Drug Discovery" by S.J. Mahdizadeh, and L.A. Eriksson (https…☆17Jun 14, 2024Updated last year
- Plausibility checks for generated molecule poses.☆355Feb 9, 2026Updated 2 weeks ago
- Simple protein-ligand complex simulation with OpenMM☆94Sep 6, 2023Updated 2 years ago
- ☆29Jul 28, 2023Updated 2 years ago
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆20Oct 2, 2024Updated last year
- ☆29May 5, 2025Updated 9 months ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆154Feb 17, 2026Updated last week
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆164Feb 1, 2026Updated 3 weeks ago
- MoleculeKit: Your favorite molecule manipulation kit☆235Updated this week
- Algorithm for identifying hydrogen bond networks in CG proteins to implement Go-like Martini 3 models☆15Oct 25, 2024Updated last year
- Contributed and additional nodes for maize☆21Feb 18, 2026Updated last week
- This repository provides an implementation of the DTi2Vec tool, to identify Drug-Target interaction using network embedding and ensemble …☆12Sep 28, 2021Updated 4 years ago
- ☆13Apr 15, 2024Updated last year
- A new python package to visualize molecules in dots hover☆13Feb 15, 2024Updated 2 years ago
- Python code that takes a SDF file as input to calculate the central nervous system multiparameter optimization (CNS MPO) score☆11Oct 23, 2018Updated 7 years ago
- AutoGraph: autonomous graph based clustering of metabolite conformations☆12Mar 25, 2022Updated 3 years ago