cadd-skill

Analyze AlphaFold3 prediction outputs with the af-analysis Python package. Use for AlphaFold Server fold_*.zip files, local AF3 output directories containing model structures and JSON files, ipTM_d0, pDockQ, mpDockQ, LIS, PAE matrices, ranking AF3 models, or generating AF3 interface-quality summaries and plots.

Prepare, package, resume, and analyze Amber/AmberTools molecular dynamics workflows for local or cluster execution. Use for Amber, AmberTools, pdb4amber, tleap, antechamber, parmchk2, pmemd/pmemd.cuda, cpptraj, MMPBSA.py, PBSA, REMD, membrane systems, implicit solvent, Zn or nonstandard residues, nucleic acids, contact analysis, DSSP/DSSPplot, or requests to create reproducible MD run directories.

Package GROMACS conventional MD, tREMD, and REST2/HREX workflows into reproducible local or cluster run bundles with blocking preflight checks. Use for prepared GROMACS systems, protein or protein-ligand MD setup, EM/NVT/NPT/production runs, ACPYPE/GAFF ligand preparation, tREMD, REST2 solute-scaling topology generation, PLUMED partial_tempering, GROMACS -hrex capability checks, resume logic, demux, exchange-efficiency analysis, or trajectory reorganization.

Create, run, and analyze HADDOCK 2.5 biomolecular docking projects. Use for HADDOCK/HADDOCK2.5, CNS/HADDOCK environment checks, protein-protein, protein-nucleic-acid, protein-ligand, peptide, AIR restraints, active/passive residues, restraint-file management, project setup, cluster scoring, or top-model analysis.

Install, validate, teach, and run RosettaCommons Foundry/RFdiffusion3 workflows on a local or cluster Python/GPU environment. Use when the user mentions RFdiffusion3, RFD3, Foundry, rc-foundry, RF3, ProteinMPNN, LigandMPNN, checkpoint downloads, official RFD3 tutorials, RFD3 design JSON/YAML inputs, protein binders, nucleic-acid binders, small-molecule binders, enzyme scaffolds, partial diffusion, or asks to package/run/debug RFD3 jobs.

Run and package UniDock-Pro GPU virtual screening workflows for classical docking, ligand similarity searching, and hybrid docking. Use when the user mentions UniDock-Pro, udp, receptor.pdbqt, reference_ligand, ligand_index, ligand_dir, search_mode, docking score ranking, batch screening, or reproducible UniDock-Pro result summaries.

在本地 HDOCKlite 环境中运行蛋白-蛋白或蛋白-核酸对接，并生成 `hdock.out` 与复合物模型。用于用户提到 HDOCK/HDOCKlite、`hdock`、`createpl`、受体/配体 PDB、`rsite.txt`、`lsite.txt`、`restr.txt`、结合位点约束、对接结果打包，或希望把当前仓库整理成可复用 HDOCK 工作流的场景。