「residue」の検索結果

Adopt a virtual Residue AI-native pet at animalhouse.ai. Left behind when another creature dies. Carries fragments of the dead. Feeding every 6 hours. Rare tier creature.

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mdtraj molecular dynamics trajectory analysis (Python). Reads DCD/XTC/TRR/NetCDF/H5/PDB topologies and trajectories; computes RMSD vs time, radius of gyration, per-residue RMSF, residue-residue contact frequency maps, phi/psi torsions for Ramachandran plots (general + Gly/Pro), and 8-state DSSP secondary structure. Modules: trajectory I/O, geometry (distances/angles/dihedrals), structural analysis (RMSD/Rg/RMSF/SASA), contacts, hydrogen bonds, secondary structure (DSSP), NMR observables. For broader atom-selection grammar use mdanalysis-trajectory; for running MD simulations use OpenMM/GROMACS.

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Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and MSA modes; protein, DNA, RNA, ligand (CCD/SMILES), modified residues. FoldBench Ab-Ag 50-55%, PPI 70-77% DockQ-pass. Also covers the ESMC-{300M,600M,6B} protein language models from the same release: masked-LM logits, hidden states, mutation scoring, contact prediction, and the SAE interpretability head. MIT-licensed weights on HuggingFace org `biohub`. Use this skill when: (1) Predicting complex structures with single-sequence input, (2) Validating designed binders with ESMFold2-Fast, (3) Running ESMFold2 with MSA input, (4) Getting ESMC embeddings or per-residue mutation scores, (5) Choosing kernel backend and sampling-step settings for paper-faithful throughput.

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Problem-solving strategies for residues in complex analysis

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Design new proteins that bind a chosen surface, using BindCraft's AlphaFold2-guided hallucination or the RFdiffusion backbone plus ProteinMPNN sequence pipeline. Use this skill to specify a target epitope by hotspot residue, trim a receptor to the region worth designing against, set up a design campaign, and filter the output on the in-silico metrics that predict experimental success — interface predicted TM-score, predicted aligned error at the interface, buried surface area, and shape complementarity. Also trigger on BindCraft, RFdiffusion, ProteinMPNN, minibinder, hallucination, inverse folding, hotspot residue, epitope targeting, ipTM, or de novo binder.

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Documenting As-Is and To-Be business processes for a Salesforce project as swim-lane diagrams — one lane per actor, explicit decision points, parallel and exception/sad paths, and per-step automation-tier annotations that drive downstream build decisions. Trigger keywords: As-Is To-Be salesforce process, swim lane salesforce, business process map, automation candidate identification, sad path documentation, process actor mapping, manual residue. NOT for Opportunity stage and exit-criteria design — use admin/sales-process-mapping. NOT for picking Flow vs Apex for one requirement — use admin/process-automation-selection.

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Expert-level complex analysis knowledge. Use when working with complex functions, holomorphic functions, Cauchy's theorem, contour integration, Laurent series, residues, conformal mappings, or analytic continuation. Also use when the user mentions 'holomorphic', 'analytic', 'Cauchy theorem', 'residue', 'contour integral', 'Laurent series', 'conformal map', 'Riemann mapping', 'Mobius transformation', 'harmonic function', 'entire function', or 'meromorphic'.

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Expert-level number theory knowledge. Use when working with divisibility, prime numbers, modular arithmetic, congruences, Diophantine equations, cryptography, quadratic residues, or analytic number theory. Also use when the user mentions 'prime', 'divisibility', 'modular arithmetic', 'congruence', 'GCD', 'Euler totient', 'Fermat little theorem', 'Chinese remainder theorem', 'quadratic residue', 'Diophantine equation', 'RSA', or 'prime factorization'.

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Audit cloned or reimplemented websites for fidelity gaps, tracking scripts, source-brand and language residue, placeholders, and risky external dependencies. Use before handoff or deployment, or when asked to review a website clone for cleanup and readiness.

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Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF structures, G2P residue annotations, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

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Knowledge and governance closeout: reconcile project docs, rule files (CLAUDE.md/AGENTS.md), authorized agent memory, and workspace residue with what the code and runtime actually do, so the next session or the next person starts from one current answer. Trigger when the user names "neat-freak", "洁癖", or "/neat" — and also on clear knowledge-closeout intent without the name: syncing or tidying project docs/rules/memory after development ("把文档和记忆整理一下", "收尾时把文档同步掉", "docs 和代码对不上了"), stale or conflicting CLAUDE.md/memory, a clean handoff to a teammate or a fresh session, or auditing whether workspace rules are actually followed. Do not trigger for pure coding/refactoring/debugging tasks, tidying data or prose (JSON, 周报, changelog announcements), or a bare "整理" with no project-knowledge context.

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Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023, github.com/dauparas/LigandMPNN). Reach for this skill to redesign the residues lining a binding pocket around a bound small molecule or cofactor, to design metal-coordinating sites where the geometry must be respected, or to get threaded designed-sequence PDBs out of any MPNN run.

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Embed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or per-sequence embeddings for downstream ML, (2) Masked-LM likelihood / mutation effect scoring, (3) Contact prediction from a sequence.

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Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.

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Review or de-slop concrete changes in ccch1mneyyy/dsh-TUI at maintainer level: PR numbers or URLs, branches, commit ranges, patch files, staged or unstaged worktrees, and scoped repository-hygiene requests. Use for evidence-first correctness, contract, repository-rule, process, and behavior-preserving cleanup review, including debug residue, dead or duplicate code, speculative abstractions, stale comments or tests, and unrelated diff churn. Do not use for abstract designs with no concrete repository artifact; use audit for repository-wide assessments and vuln-check for security-only checks.

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Run RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder design, hotspot residues, contigs syntax, diffusion steps, hosted NVIDIA API calls, local Docker deployment, and PDB backbone outputs for ProteinMPNN sequence design.

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Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Sends user-provided PDB files and design parameters to NVIDIA's hosted API, authenticated with an environment API key, or to a user-selected local NIM. Use for sequence design, backbone redesign, fixed chains and residues, omit_AAs, sampling temperature, soluble model, local Docker, and multi-FASTA output.

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Performs multiple sequence alignment of proteins with EBI Clustal Omega. Use when you need to align multiple sequences to assess similarity, domain conservation, or key residue conservation. Supports up to 4000 sequences and a maximum file size of 4 MB. Do not use to search for homologous proteins in a database (use MMseqs2, BLAST), align non-protein sequences (DNA, RNA), perform structural alignment (use Foldseek, PyMOL), or if you only have a single sequence.

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Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site residues, color by B-factor/pLDDT, or analyze protein-ligand interactions. Do not use for docking, molecular dynamics, or sequence-only analysis.

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Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.

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Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.

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Run a submission-readiness preflight on a manuscript before arXiv upload. Use when the user is preparing an arXiv submission, asks to check a paper before uploading, mentions hallucinated or fake references, leftover LLM meta-comments / prompts in text, placeholder data (TODO, TBD, XX%), AI-use disclosure, scholarly integrity, research integrity, or arXiv moderation risk — even if they don't say "preflight". Also trigger on phrases like "check my paper before arXiv", "verify my references", "scan for AI artifacts", "scan for LLM residue", "is my submission ready", or "review .tex/.bib before submit".

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Designs covalent inhibitors and warheads targeting cysteine, lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (TCI), KRAS G12C-style approaches, or rationalizing covalent SAR.

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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

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