benchaid

Predict optimal construct boundaries for protein expression. Use when the user asks about domain boundaries, construct design, truncations, which region of a protein to express, or identifying disordered regions.

Manage lab notebook entries, registry items (plasmids, proteins, etc.), templates, widgets, and audit logs via the Labbook service. Use when creating or viewing lab notebook entries, managing the sample registry, or documenting experiments.

Verify open reading frames (ORFs) in plasmid sequences. Use when the user asks about verifying protein coding sequences, checking if an ORF is present in a plasmid, finding where a protein is encoded, or doing six-frame translation analysis.

Fetch sequencing data from Plasmidsaurus. Use when the user asks about listing sequencing orders, downloading sequencing results, checking order status, or retrieving plasmid sequences from Plasmidsaurus.

Design PCR primers for molecular cloning. Use when the user asks about designing primers, LIC cloning primers, sequencing primers, Gibson assembly primers, or working with NCBI accession codes for cloning.

Calculate protein parameters (MW, pI, extinction coefficient) and generate purification recommendations. Use when the user asks about protein properties, molecular weight, isoelectric point, extinction coefficients, or purification strategies.

Decision trees and workflows for molecular cloning in structural biology labs. Use when the user asks about cloning strategies, LIC vs Gibson, biGBac assembly, tag selection, expression system choice (insect vs E. coli), codon optimization, or designing constructs.

Query and manage Quartzy lab inventory, order requests, and webhooks. Use when the user asks about lab supplies, reagent inventory, placing orders, checking order status, or creating new order requests in Quartzy.

Calculate reaction buffer recipes accounting for protein stock contributions. Use when the user asks about designing reaction buffers, calculating buffer volumes, compensation buffers, or setting up biochemistry experiments with proteins.

Codon optimize protein sequences for expression using IDT's API. Use when the user asks to codon optimize genes, sequences, or accessions for a target organism (insect, E. coli, mammalian, yeast) or vector (438, 1-, pVEX).

Assemble and purify macromolecular complexes for structural biology. Use when the user asks about gel filtration, complex assembly, SEC purification, elongation complexes, calculating stoichiometry, or interpreting A260/A280 ratios.

Generate expected plasmid maps by combining vector backbones with insert sequences. Use when the user asks about in-silico cloning, simulating cloning reactions, generating construct maps, or verifying clone sequences against expected products.

Baculovirus expression system for recombinant protein production. Use when the user asks about insect cell expression, baculovirus, V0/V1 production, Sf9/Hi5/Sf21 cells, DH10αEMBacY transfection, or large-scale protein expression.

Search, read, and download from Notion. Use when the user asks about protocols, lab databases, or needs to download files (like vector maps) from Notion.

Parse SnapGene .dna files. Use when the user asks to read, convert, or extract information from SnapGene files, or needs to convert .dna to GenBank/FASTA format.

Order DNA synthesis from Twist Bioscience. Use when the user asks to order clonal genes, gene blocks, or gene fragments from Twist, or to submit codon-optimized sequences for synthesis.

Annotate SDS-PAGE gel images with molecular weight markers and lane labels. Use when asked to label, annotate, or analyze gel photos. Detects lanes and bands automatically via intensity profiling (scikit-image), assigns MW from known protein ladders, and outputs SVG-quality annotated images.

PHENIX suite for macromolecular structure determination. Use for cryo-EM model building, real-space refinement, map analysis, validation, and AlphaFold model processing.

Servalcat for cryo-EM SPA reciprocal-space refinement and Fo-Fc map calculation. Use for refining models against half-maps, calculating weighted difference maps, and omit maps.

Print labels on the lab's Zebra ZD411 printer (2"x1" labels). Use when asked to print labels, tube labels, box labels, sample labels, or anything involving the Zebra/label printer. Supports text labels, barcodes, and raw ZPL.