PDBeurope / ccdutilsLinks
A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit
☆65Updated 2 weeks ago
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☆105Updated 11 months ago
- Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina☆52Updated 2 months ago
- ☆68Updated last year
- All in one Structure-Based Virtual Screening workflow based on the concept of consensus docking.☆47Updated 6 months ago
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆113Updated 9 months ago
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆27Updated this week
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆57Updated 2 weeks ago
- Fully automated high-throughput MD pipeline☆69Updated this week
- Ligand-Protein Interaction Mapping☆60Updated 3 months ago
- Simple protein-ligand complex simulation with OpenMM☆87Updated last year
- ☆93Updated 6 months ago
- ☆45Updated 3 months ago
- Fast and accurate molecular docking with an AI pose scoring function☆41Updated last year
- Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention☆53Updated 2 months ago
- A benchmark for 3D biomolecular structure prediction models☆64Updated 3 months ago
- pythonic interface to virtual screening software☆89Updated 2 years ago
- FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.☆54Updated last year
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆52Updated 3 months ago
- ☆33Updated 2 years ago
- ☆63Updated 4 months ago
- Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file☆34Updated last month
- Trusted force field files for gromacs☆57Updated 9 months ago
- Fully automated docking pipeline (can be run in distributed environments)☆47Updated this week
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆71Updated 7 months ago
- Structure prediction and design of proteins with noncanonical amino acids☆88Updated 3 weeks ago
- Scores for Hydrophobicity and Charges based on SASAs☆36Updated 2 months ago
- Training and inference code for ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design [ICLR 2025 ora…☆77Updated last month
- Quick mapping of Uniprot sequences to PDB structures☆33Updated 4 months ago
- ☆49Updated 8 months ago
- FeatureDock is a protein-ligand docking software guided by physicochemical feature-based local environment learning using Transformer☆35Updated 10 months ago