439 skills found · Page 1 of 15
pharmai / PlipProtein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361
saeyslab / NichenetrNicheNet: predict active ligand-target links between interacting cells
dauparas / LigandMPNNNo description available
chemosim-lab / ProLIFInteraction Fingerprints for protein-ligand complexes and more
ventolab / CellphoneDBCellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
rdk / P2rankP2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
jensengroup / PropkaPROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
zrqiao / NeuralPLexerNeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
luwei0917 / DynamicBindrepo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
plinder-org / PlinderProtein Ligand INteraction Dataset and Evaluation Resource
patrickbryant1 / UmolProtein-ligand structure prediction
saezlab / LianaLIANA: a LIgand-receptor ANalysis frAmework
CAODH / SurfDockSurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction
baker-laboratory / PLACERPLACER is graph neural network for local prediction of protein-ligand conformational ensembles.
GHeinzelmann / BAT.pyThe Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RBFE) calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.
openforcefield / Protein Ligand BenchmarkProtein-Ligand Benchmark Dataset for Free Energy Calculations
BioinfoMachineLearning / PoseBenchComprehensive benchmarking of protein-ligand structure prediction methods. (Nature Machine Intelligence)
zaixizhang / PocketGenPocketGen (Nature Machine Intelligence 24): Generating Full-Atom Ligand-Binding Protein Pockets
ingcoder / UnomdPython package to run molecular dynamics simulation of a protein-ligand complex in a single line of code.
wolberlab / OpenMMDLInterface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes
