Skill UI

Biopython provides Python APIs for sequence manipulation, database access, BLAST automation, structural bioinformatics, and phylogenetics, making it ideal for scripting custom pipelines and batch processing in computational molecular biology workflows.

DeepChem is a Python library for molecular machine learning, providing featurizers, dataset loaders, splitters, and models spanning traditional ML to GNNs for property prediction, drug discovery, and materials design.

Molfeat is a Python toolkit that converts SMILES/RDKit molecules into embeddings via 100+ calculators, transformers, and pretrained models for QSAR, screening, similarity search, and deep learning pipelines.

Access RCSB PDB to search biomolecular structures via text, sequence, or geometry queries, download coordinate files in PDB/mmCIF/Binary formats, retrieve metadata, and batch-process entries for drug discovery, protein engineering, and structural biology pipelines.

Provides AI-ready drug discovery datasets, splits, and benchmarks covering ADME, toxicity, DTI, DDI, and molecular generation so researchers can train, compare, and optimize therapeutic ML models with curated splits and oracles.

RDKit delivers a Python-based cheminformatics toolkit for parsing SMILES/SDF, computing descriptors, generating 2D/3D coordinates, fingerprinting, searching substructures, managing reactions, and visualizing molecules, ideal for drug discovery and computational chemistry workflows.

Cloud-native Rowan orchestrates medicinal chemistry and molecular modeling pipelines via a Python API, offering pKa prediction, docking, descriptors, dynamics, and AI-driven structure workflows for scalable batch screening without local HPC.

Run OpenMM-powered molecular dynamics simulations and MDAnalysis trajectory workflows to build protein or small-molecule systems, minimize energy, equilibrate conditions, and characterize RMSD/RMSF, contacts, and free-energy surfaces for structural biology or drug studies.

A comprehensive toolkit for reconstructing and analyzing the evolutionary history of biological sequences (genes, proteins, genomes). The standard workflow includes multiple sequence alignment using MAFFT, robust maximum likelihood tree inference with IQ-TREE 2 and FastTree, and advanced visualization/manipulation using ETE3. This skill is essential for studies in viral phylodynamics, microbial genomics, protein family evolution, and molecular clock dating.

Biopython is a robust, comprehensive toolkit for computational molecular biology written in Python. It enables users to manipulate biological sequences (DNA, RNA, protein), parse standard formats (FASTA, GenBank, PDB, etc.), and programmatically access major bioinformatics databases like NCBI via Entrez. This skill is ideal for developing complex bioinformatics pipelines, including sequence alignment, structural analysis, and phylogenetic tree construction.

Datamol provides a simplified, Pythonic abstraction layer over RDKit, making complex molecular operations accessible for chemical data science. It supports core functionalities including SMILES parsing, structure standardization, calculation of molecular descriptors (e.g., LogP, MW), 3D conformer generation, and efficient parallel batch processing. It is ideal for streamlining molecular data handling in drug discovery and chemical research pipelines.

DeepChem is a comprehensive Python library designed for applying machine learning to complex fields like chemistry, materials science, and biology. It enables users to perform molecular property prediction (e.g., ADMET, toxicity), train models using specialized graph neural networks (GNNs), and process diverse molecular formats (SMILES, SDF, FASTA). It provides extensive featurization options, making it foundational for drug discovery and computational chemistry research.