Chem Similarity Search
Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.
General Fair Data Review
Review a manuscript or code repository for FAIR data compliance (Findable, Accessible, Interoperable, Reusable), producing a structured report with pass/fail per principle and actionable remediation steps.
Chem Sorption Relax
Prepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools.
Drug Admet Prediction
Compute RDKit physicochemical descriptors and rule-based drug-likeness heuristics (Ro5, Veber, QED) from SMILES.
General Arxiv Search
Search and retrieve research papers from ArXiv API for scientific research.
Chem Dft Orca Singlepoint
Run a DFT or Coupled Cluster single-point energy calculation (with optional gradients/Hessian) on a molecular structure with ORCA through SCINE wrapper.
Drug Pocket Detection
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Drug Mmpbsa Gbsa
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Chem Hazard Toxicity
Extract explicit safety warnings, GHS classifications, and LD50 profiles from PubChem PUG VIEW.
Chem Conformer Search
Generate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.
Chem Msms Predict
Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.
Chem Db Spectra
Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.
Chem Ts Optimization
Optimize non-periodic molecular TS guesses and verify first-order saddle point from vibrational modes.
Drug Docking Vina
Dock small-molecule ligands into a protein receptor using AutoDock Vina (Python API) and save ranked poses + docking metadata for reproducible virtual screening.
Chem Sorption Widom
Calculates Henry coefficient and heat of adsorption for a gas in a porous framework using Widom insertion with any supported MLIP.
General Chemical Literature
Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.
Chem Solution Md
Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.
Drug Complex System Builder
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General Biorxiv Search
Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.
Chem Nmr Predict
Predict 1H NMR spectra from SMILES strings via NMRdb.org SPINUS neural network prediction and nmrsim quantum mechanical spin simulation.
Chem Db Mof
Query multiple MOF databases (QMOF via MPContribs; ARC-MOF DB7/Majumdar et al. via Zenodo) and download CIF structures with optional element or identifier filters.
General Deep Research
Perform iterative, deep, and comprehensive literature research on a specific materials/chemistry topic.
Chem Sorption Gcmc
Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.
Chem Dft Orca Optimization
Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.
Drug Trajectory Analysis
Analyze a protein-ligand MD trajectory to compute ligand RMSD, pocket RMSF, hydrogen bonds, contact occupancy, and protein-ligand interaction fingerprints over time.
Drug Db Chembl
Query ChEMBL web services for targets, molecules, and curated bioactivity measurements (IC50, Ki, EC50, etc.).
Drug Protein Ligand Md
Run a protein-ligand MD simulation in OpenMM with energy minimization, restrained equilibration, and production NPT, producing trajectory and checkpoint files for downstream analysis.
Drug Protein Prep
Prepare macromolecular receptor structures (PDB/mmCIF or RCSB PDB ID) for docking or simulation by fixing common structure issues and adding hydrogens.
Drug Docking Analysis
Post-docking analysis of virtual screening results including score distributions, enrichment metrics (ROC AUC, enrichment factors), and ligand efficiency calculations.
Drug Db Pdb
Search, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads.
Chem Spectrum Matcher
Match an experimental spectrum (1H NMR, 13C NMR, IR) against predicted or database reference spectra for candidate ranking and structure confirmation. Supports local catalog lookup, public database fallback, and pluggable similarity metrics.
Drug Molecular Fingerprints
Compute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.
Chem Neb Barrier
Calculate activation barrier using Nudged Elastic Band (NEB) method with MLIPs.
Chem Nmr Analysis
Scripts for Wasserstein deconvolution of 1H NMR mixture spectra against reference spectra, reaction product prediction, time-series kinetics, and spectral plotting.
Drug Redocking Rmsd
Compute symmetry-corrected heavy-atom RMSD between docked poses and a reference crystal ligand to validate docking protocols.
Chem Vibration
Calculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.
General Chemical Pricing
Retrieves averaged elemental prices and provides direct vendor purchase links for elements and precursor compounds.
Drug Binding Site Definition
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Drug Pose Validation
Validate docked or generated ligand poses for physical plausibility using PoseBusters, filtering out chemically invalid or clashing poses before downstream refinement.
Drug Db Pubchem
Query PubChem via PUG-REST to retrieve CIDs, computed properties, synonyms, and 2D/3D SDF structures.
Drug Ligand Prep
Prepare small-molecule ligands for docking and analysis via optional state enumeration, 3D conformer generation, MMFF/UFF minimization, and export to SDF + AutoDock PDBQT.
Chem Bond Dissociation
Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.
Drug Bioactivity Assay
Fetch biological assays and target proteins a chemical has been tested against via PubChem.
Chem Thermochemistry
Compute gas-phase thermodynamic quantities (H, S, G) and reaction thermochemistry (ΔH, ΔS, ΔG) using MLIPs with the ideal-gas/rigid-rotor/harmonic-oscillator approximation.
Chem Db Qmof
Query the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.
Chem Docking Void
Dock small-molecule guests into a porous host material using the VOID library (Voronoi Clustering), generating multiple 3D conformers with RDKit and ranking generated complexes.
Drug Retrosynthesis
Predict synthetic accessibility and retrosynthetic pathways for novel molecules using the IBM RXN API.
Chem Dft Orca Advanced Calculation
Write and run custom ORCA input files for advanced electronic structure methods or settings not available through the SCINE wrapper, including multi-reference methods, excited states, relativistic effects, advanced SCF, NMR/EPR, and more.
Chem Irc Verification
Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.
Chem React Ot
Generate transition state structures for chemical reactions using React-OT.