kdevos12/alkyl
27 skills
$npx skills add kdevos12/alkylSkillInstalls
active-learningUse when designing active learning or closed-loop molecular optimization (DMTA cycles).aseUse when working with ASE (Atomic Simulation Environment) for atomistic simulations.binding-kineticsUse when analyzing or predicting drug-target binding kinetics: kon, koff, KD, residence time, SPR data fitting (Langmuir/two-state), ITC thermodynamics,…chem-brainstormUse at the start of any computational chemistry task to structure thinking, map available tools, and generate concrete hypotheses.coarse-grainedUse when running coarse-grained (CG) molecular dynamics with MARTINI 3.daylight-theoryUse when working with SMILES, SMARTS, SMIRKS, molecular fingerprints, or cheminformatics fundamentals.deepchemUse when working with DeepChem for molecular machine learning, drug discovery, quantum chemistry, materials science, or bioinformatics.dockingUse when performing protein-ligand docking, virtual screening, or structure-based drug design.fbddUse for fragment-based drug design (FBDD): Rule of 3 filtering, ligand efficiency metrics (LE/LLE/BEI/LELP), fragment library design, fragment docking…force-fieldsUse when working with molecular mechanics force fields for MD simulations.free-energyUse when computing free energy differences for drug discovery.generative-designUse when designing or evaluating generative models for de novo drug/molecule design.homology-modelingUse when building a 3D protein structure from sequence (no experimental structure available).lit-rescueLast-resort skill. Invoke when no obvious or coherent solution is available and hallucination risk is high.mdanalysisUse when analyzing molecular dynamics trajectories with MDAnalysis.mmpaUse when performing Matched Molecular Pair Analysis (MMPA) for SAR extraction, property cliff identification, bioisostere discovery, or analogue generation.nextflowUse when writing, debugging, or optimizing Nextflow pipelines for computational chemistry, bioinformatics, or HPC workflows.openbabelUse when converting molecular file formats, generating 3D coordinates, searching conformers, computing descriptors/fingerprints, or filtering chemical…organic-mechanismsUse when reasoning about polar organic reaction mechanisms, arrow pushing, SN1/SN2/E1/E2, nucleophile/electrophile identification, Zaitsev/Hofmann selectivity,…pepflexUse when working with PepFlex for in silico peptide screening and evolutionary optimization.pharmacophoreUse when working with pharmacophore modeling for drug discovery.py3DmolUse when creating 3D molecular visualizations with py3Dmol (3Dmol.js).qm-dftUse when working with quantum chemistry (QM) and DFT calculations.rdkitUse when working with RDKit for cheminformatics in Python. Covers molecular I/O, property calculation, Lipinski filters, fingerprints, similarity, 3D conformer…synkitUse when working with SynKit for graph-based reaction informatics: ITS/MTG graph construction, reaction canonicalization, AAM validation, DPO rule extraction…torchdrugUse when working with TorchDrug for graph-based drug discovery and molecular ML.uncertainty-qsarUse when building QSAR/ML models that need calibrated uncertainty estimates.