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THE SKILLS DIRECTORY

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274 项技能filling

bio-structural-biology-structure-preparation

bio-structural-biology-structure-preparation

【效率与协作】Prepares a deposited or predicted structure for docking, molecular dynamics, or electrostatics by adding hydrogens, assigning protonation and tautomer states, and filling missing atoms and short loops with PDBFixer, reduce, PROPKA, and PDB2PQR. Use when adding hydrogens an X-ray model never resolved; assigning His HID/HIE/HIP tautomers, Asn/Gln/His 1…

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bio-systems-biology-metabolic-reconstruction

bio-systems-biology-metabolic-reconstruction

【效率与协作】Builds draft genome-scale metabolic models from an annotated genome using CarveMe (top-down carving of a BiGG universal model) or gapseq (bottom-up pathway-evidence reconstruction), then loads and sanity-checks the draft in COBRApy. Use when creating a model for an organism without one, choosing between CarveMe and gapseq, gap-filling to a target med…

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bio-workflows-metabolic-modeling-pipeline

bio-workflows-metabolic-modeling-pipeline

【开发与工程】Orchestrates genome-scale metabolic modeling from a protein FASTA to flux predictions, chaining CarveMe/gapseq reconstruction, memote QC, gap-filling, media-constrained FBA/FVA, gene essentiality, and context-specific models. Use when committing the reconstruction tool (which locks the identifier NAMESPACE forever - BiGG vs ModelSEED vs KEGG, no auto…

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