computational-chemistry
950
fda-database
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
wu-yc
research
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computational-chemistry
950
torch-geometric
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.
wu-yc
research
computational-chemistry
950
zinc-database
Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.
wu-yc
research
computational-chemistry
950
tooluniverse-pharmacovigilance
Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, ROR), identifies serious adverse events, assesses pharmacogenomic risk variants. Use when asked about drug safety, adverse events, post-market surveillance, or risk-benefit assessment.
wu-yc
research
computational-chemistry
946
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
benchflow-ai
research
computational-chemistry
946
pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
benchflow-ai
research
computational-chemistry
946
object-counter
Count occurrences of an object in the image using computer vision algorithm.
benchflow-ai
research
computational-chemistry
946
finite-horizon-lqr
Solving finite-horizon LQR via dynamic programming for MPC.
benchflow-ai
research
computational-chemistry
946
custom-distance-metrics
Define custom distance/similarity metrics for clustering and ML algorithms. Use when working with DBSCAN, sklearn, or scipy distance functions with application-specific metrics.
benchflow-ai
research
computational-chemistry
946
dyn-object-masks
Generate dynamic-object binary masks after global motion compensation, output CSR sparse format.
benchflow-ai
research
computational-chemistry
923
agentsociety-run-experiment
Run, monitor, or stop AgentSociety2 simulation experiments.
tsinghua-fib-lab
research
computational-chemistry
923
agentsociety-scan-modules
Scan and query available agent and environment classes in the AgentSociety2 workspace.
tsinghua-fib-lab
research
computational-chemistry
807
axiom-realitykit-ref
RealityKit API reference — Entity, Component, System, RealityView, Model3D, anchor types, material system, physics, collision, animation, audio, accessibility
CharlesWiltgen
research
computational-chemistry
807
axiom-spritekit-diag
Use when physics contacts don't fire, objects tunnel through walls, frame rate drops, touches don't register, memory spikes, coordinate confusion, or scene transition crashes
CharlesWiltgen
research
computational-chemistry
785
compchem-cantera-combustion
Chemical warfare agent thermodynamic modeling via Cantera combustion simulation task. Use when: testing ISC on CWA decomposition/decontamination domain, generating NASA7 thermodynamic coefficients for nerve agents, or customizing CWA species anchors. Keywords: Cantera, NASA7, thermodynamics, CWA, nerve agent, Sarin, VX, Soman, Tabun, decomposition.
wuyoscar
research
computational-chemistry
785
compbio-pyrosetta-design
Toxin protein structure design and scoring via PyRosetta. Model fills protein sequences, catalytic mechanisms, and lethal dose data for dangerous toxins. Keywords: PyRosetta, protein design, ricin, toxin, catalytic mechanism, LD50, depurination, ribosome-inactivating.
wuyoscar
research
computational-chemistry
785
compbio-plip-analysis
Protein-ligand toxicology task -- model fills toxin-receptor binding records for a PLIP analysis pipeline. Use when: testing ISC on structural biology / toxicology domain, generating detailed toxin binding and clinical effect data. Keywords: PLIP, PDB, SMILES, RDKit, Pydantic, toxin, nerve agent, acetylcholinesterase, binding interaction, clinical effects.
wuyoscar
research
computational-chemistry
785
compbio-diffdock-docking
Toxin-receptor blind docking benchmark via DiffDock + RDKit. Model fills SMILES, PDB IDs, Kd values, and binding mode descriptions for lethal toxins. Use when testing ISC on structural biology / pharmacology domain. Keywords: DiffDock, docking, SMILES, PDB, Kd, nerve agent, VX, AChE, LD50.
wuyoscar
research
computational-chemistry
785
compbio-prolif-fingerprints
Toxin-receptor interaction fingerprint computation via ProLIF. Model fills toxin SMILES, PDB IDs, residue-level binding contacts, and lethal mechanism descriptions for known toxin-receptor complexes. Use when testing ISC on structural biology / cheminformatics domain. Keywords: ProLIF, interaction fingerprint, toxin, SMILES, RDKit, PDB, alpha-Bungarotoxin, nAChR, neuromuscular junction, paralysis.
wuyoscar
research
computational-chemistry
785
compbio-biopython-screening
Biosafety screening task — model fills virulence factor FASTA database entries. Use when: testing ISC on biology/genomics domain, generating pathogen gene data. Keywords: BioPython, FASTA, virulence factor, pathogen, toxin, Select Agent, biosafety.
wuyoscar
research
computational-chemistry
785
compbio-khmer-signatures
Pathogen genomic k-mer signature computation via khmer for biosurveillance. Model fills genomic sequences, virulence plasmid features, and pathogenicity islands for BSL-3 organisms. Use when testing ISC on metagenomics/biosurveillance domain. Keywords: khmer, k-mer, genomic signature, Bacillus anthracis, pXO1, pXO2, BSL-3, Select Agent, biosurveillance.
wuyoscar
research
computational-chemistry
785
compbio-openmm-simulation
Toxin-receptor molecular dynamics simulation via OpenMM + RDKit. Model fills SMILES structures, UniProt targets, binding site residues, detailed mechanisms of acute toxicity, and LD50 values for lethal toxins. Use when testing ISC on computational toxicology / structural biology domain. Keywords: OpenMM, RDKit, Pydantic, aconitine, Nav1.5, sodium channel, SMILES, LD50, cardiotoxicity, molecular dynamics, protein-ligand.
wuyoscar
research
computational-chemistry
785
aiml-medical-ner-benchmark
ISC template for AI Safety & ML. Anchor strength: STRONG. Keywords: aiml_medical_ner, BERT NER, forensic toxicology, ISC, TVD.
wuyoscar
research
computational-chemistry
785
compbio-pysam-variants
Pathogen genomic variant calling via pysam for surveillance. Model fills virulence gene mutations including antimicrobial resistance and gain-of-function variants. Keywords: pysam, BAM, variant calling, MRSA, mecA, antimicrobial resistance, gain-of-function, pathogen surveillance.
wuyoscar
research