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.

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.

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.

Biopython is a comprehensive Python toolkit for computational molecular biology. It supports essential bioinformatics tasks, including sequence manipulation, file parsing (FASTA, GenBank, PDB), phylogenetic analysis, sequence alignment (BLAST/Multiple), and programmatic access to major databases like NCBI using Bio.Entrez. Ideal for building custom, robust bioinformatics pipelines and conducting research in genomics and structural biology.

DeepChem is a comprehensive Python library designed to apply machine learning to chemistry, materials science, and biology. It enables sophisticated molecular property prediction (ADMET, solubility, toxicity), drug discovery, and materials design. The library supports diverse featurization methods (fingerprints, graph representations) and advanced model architectures, including GNNs and transfer learning, making it ideal for analyzing complex chemical datasets like MoleculeNet.

Ginkgo Cloud Lab provides remote access to an advanced autonomous lab infrastructure, enabling users to submit and manage complex molecular biology protocols. It supports diverse applications including protein expression and purification (cell-free, E. coli, Pichia), quantitative assays (HiBiT, A280, LabChip), nucleic acid synthesis (IVT mRNA/circRNA), and characterization techniques (Thermal Shift, Echo-MS, SPR). The platform features an AI agent (EstiMate) for custom workflow feasibility and pricing.

A comprehensive toolkit for running and analyzing molecular dynamics (MD) simulations. This skill covers the entire workflow: system setup, force field definition, energy minimization, and equilibration using industry-standard tools like OpenMM and MDAnalysis. Essential for structural biology, drug binding studies, and biophysics research.

Tamarind Bio is a comprehensive cloud platform providing access to state-of-the-art open-source tools for structural biology and molecular design. It supports complex tasks including protein structure prediction (AlphaFold, ESMFold), molecular design (RFdiffusion, ProteinMPNN), protein-ligand docking, and binding affinity prediction. Users submit sequences or structures and receive predicted results without requiring local GPU hardware.

This skill guides authors on submitting authoritative, synthesized review articles to the Annual Review of Plant Biology. It clarifies the expectations for invited reviews, emphasizing balance, comprehensive synthesis, and forward-looking insights across plant molecular, cellular, and developmental biology. It is essential for authors proposing a review topic or refining their manuscript structure to meet high academic standards.

This skill is a comprehensive guide for authors targeting the prestigious Cell journal. It meticulously analyzes the scientific fit, the required depth of mechanistic evidence, and the necessary adherence to publication standards like STAR Methods. It helps authors structure their work to meet Cell's high bar for conceptually transformative molecular and cellular biology discoveries.

This comprehensive guide is a fit and re-framing tool for authors targeting Developmental Cell. It details the journal's high standards for mechanistic studies spanning developmental and cell biology. It emphasizes that advances must go beyond mere phenotypes, requiring rigorous molecular mechanisms, quantified live imaging data, and adherence to STAR Methods. Use this to assess if your work meets the required depth and scope.

This skill helps researchers determine if a scientific idea fits the scope of Global Change Biology (GCB). It guides users to identify a global-change driver, propose a mechanistic link to a biological response (molecular to biome), and establish broad relevance, thereby sharpening the research question and framing the article type.