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Chemistry

Molecular modeling and reactions.

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computational-chemistry
6.6K

pyhealth

Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
6.6K

datamol

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
6.6K

qiskit

IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
6.6K

pymatgen

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
6.6K

clinicaltrials-database

Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
6.6K

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.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
6.6K

cobrapy

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
6.6K

medchem

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
6.6K

clinical-reports

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
6.6K

awq-quantization

Activation-aware weight quantization for 4-bit LLM compression with 3x speedup and minimal accuracy loss. Use when deploying large models (7B-70B) on limited GPU memory, when you need faster inference than GPTQ with better accuracy preservation, or for instruction-tuned and multimodal models. MLSys 2024 Best Paper Award winner.

Orchestra-Research
Orchestra-Research
research
open
computational-chemistry
6.6K

gguf-quantization

GGUF format and llama.cpp quantization for efficient CPU/GPU inference. Use when deploying models on consumer hardware, Apple Silicon, or when needing flexible quantization from 2-8 bit without GPU requirements.

Orchestra-Research
Orchestra-Research
research
open
computational-chemistry
6.6K

hqq-quantization

Half-Quadratic Quantization for LLMs without calibration data. Use when quantizing models to 4/3/2-bit precision without needing calibration datasets, for fast quantization workflows, or when deploying with vLLM or HuggingFace Transformers.

Orchestra-Research
Orchestra-Research
research
open
computational-chemistry
6.6K

qdrant-vector-search

High-performance vector similarity search engine for RAG and semantic search. Use when building production RAG systems requiring fast nearest neighbor search, hybrid search with filtering, or scalable vector storage with Rust-powered performance.

Orchestra-Research
Orchestra-Research
research
open
computational-chemistry
4.5K

interpreting-culture-index

Interprets Culture Index (CI) surveys, behavioral profiles, and personality assessment data. Supports individual profile interpretation, team composition analysis (gas/brake/glue), burnout detection, profile comparison, hiring profiles, manager coaching, interview transcript analysis for trait prediction, candidate debrief, onboarding planning, and conflict mediation. Accepts extracted JSON or PDF input via OpenCV extraction script.

trailofbits
trailofbits
research
open
computational-chemistry
4.5K

yara-rule-authoring

Guides authoring of high-quality YARA-X detection rules for malware identification. Use when writing, reviewing, or optimizing YARA rules. Covers naming conventions, string selection, performance optimization, migration from legacy YARA, and false positive reduction. Triggers on: YARA, YARA-X, malware detection, threat hunting, IOC, signature, crx module, dex module.

trailofbits
trailofbits
research
open
computational-chemistry
4.2K

conducting-spearphishing-simulation-campaign

Spearphishing simulation is a targeted social engineering attack vector used by red teams to gain initial access. Unlike broad phishing campaigns, spearphishing uses OSINT-derived intelligence to craf

mukul975
mukul975
research
open
computational-chemistry
4.2K

correlating-security-events-in-qradar

Correlates security events in IBM QRadar SIEM using AQL (Ariel Query Language), custom rules, building blocks, and offense management to detect multi-stage attacks across network, endpoint, and application log sources. Use when SOC analysts need to investigate QRadar offenses, build correlation rules, or tune detection logic for reducing false positives.

mukul975
mukul975
research
open
computational-chemistry
4.2K

detecting-t1003-credential-dumping-with-edr

Detect OS credential dumping techniques targeting LSASS memory, SAM database, NTDS.dit, and cached credentials using EDR telemetry, Sysmon process access monitoring, and Windows security event correlation.

mukul975
mukul975
research
open
computational-chemistry
4.2K

detecting-wmi-persistence

Detect WMI event subscription persistence by analyzing Sysmon Event IDs 19, 20, and 21 for malicious EventFilter, EventConsumer, and FilterToConsumerBinding creation.

mukul975
mukul975
research
open
computational-chemistry
4.2K

extracting-credentials-from-memory-dump

Extract cached credentials, password hashes, Kerberos tickets, and authentication tokens from memory dumps using Volatility and Mimikatz for forensic investigation.

mukul975
mukul975
research
open
computational-chemistry
4.2K

hunting-for-persistence-via-wmi-subscriptions

Hunt for adversary persistence through Windows Management Instrumentation event subscriptions by monitoring WMI consumer, filter, and binding creation events that execute malicious code triggered by system events.

mukul975
mukul975
research
open
computational-chemistry
4.2K

implementing-anti-phishing-training-program

Security awareness training is the human layer of phishing defense. An effective anti-phishing training program combines regular simulations, interactive learning modules, metric tracking, and positiv

mukul975
mukul975
research
open
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