19 skills found
saeyslab / MultinichenetrMultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
LewisLabUCSD / Ligand Receptor PairsCompendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
jssweller / DrugHIVEDrugHIVE: Structure-based drug design with a deep hierarchical generative model
ZJUFanLab / SpaTalkKnowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
HaCTang / SiteAF3a universal molecular interaction modeling platform based on AlphaFold3, supporting structure prediction and analysis for various receptor-ligand type combinations.
ZJUFanLab / CellTalkDBA manually curated database of literature-supported ligand-receptor interactions in human and mouse
StatBiomed / SpatialDMSpatial direct messaging detected by bivariate Moran
n-szulc / FingeRNAtSoftware for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.
StatBiomed / FineSTFine-grained Spatial Transcriptomics by integrating paired histology image
genecell / LARISLARIS enables accurate and efficient ligand and receptor interaction analysis in spatial transcriptomics
fraMade / MD Ligand ReceptorMD-ligand-receptor is a bioinformatics pipeline written in Python for analyzing non-covalent ligand-receptor interactions in 3D structures starting from a molecular dynamic trajectory.
AIB001 / PRISMPRISM (Protein Receptor Interaction Simulation Modeler) is a comprehensive tool for building protein-ligand systems for molecular simulations, including MD, PMF, REST2, etc. in GROMACS, developed by ZJUIQB. It supports multiple force fields for ligands including GAFF , OpenFF, CGENFF, Opls-AA, etc. MCP server is provided for AI-Agent
durrantlab / LiggrepLigGrep is a free, open-source program for identifying docked poses that participate in user-specified receptor/ligand interactions. As input, LigGrep accepts a protein receptor file (PDB, PDBQT), a directory containing many docked-compound files (PDB, PDBQT, SDF), and a list of user-specified filters (JSON).
multitalk / ScCrossTalkInfer and visualize cell-cell communication for single-cell RNA-seq data
cyhsuTN / ScLRscLR: a method to test dysregulated ligand-receptor interactions
anasta874 / Interaction Finder Run PyMOLThe `find_interactions_PyMol_run.py` script is designed to analyze molecular interactions between a receptor and a ligand within a structure loaded in PyMOL. It automatically identifies and classifies various types of interactions, such as hydrogen bonds, hydrophobic interactions, salt bridges, van der Waals interactions, and others.
PabloPauling / Posebusters MCP ServerUnofficial MCP server for PoseBusters – validate molecular poses via HTTP or Spaces using the Model Context Protocol (MCP).
wu-2018 / ReLIVEAn interactive explorer for ligand-receptor interaction based on single-cell RNA-Seq data
UnixJunkie / LigprepLigGrep is a program for identifying docked poses that participate in user-specified receptor/ligand interactions. It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters.
