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binding-characterization

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التفرعات٠

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Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.

التثبيت

التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.

تشغيل في Manus

المصدر

BioTender-max

BioTender-max/ProteinClaw

فتح مستودع GitHub عرض مستودعات المنشئ

تنزيل

تشغيل في Manus

المهن ذات الصلةSOC

استنادا إلى تصنيف SOC المهني

علماء الكيمياء الحيوية والفيزياء الحيويةعلوم الحياة والطبيعة والاجتماع·SOC 19-1021

SKILL.md

readonly

name	binding-characterization
description	Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.
license	MIT
category	experimental
tags	["binding","spr","bli","validation"]
source	https://github.com/adaptyvbio/protein-design-skills

Binding Characterization: SPR and BLI

SPR vs BLI Decision Matrix

Factor	Choose SPR	Choose BLI
Sensitivity	Small molecules (<500 Da)	Large complexes, antibodies
Throughput	Low-medium (serial)	High (96-well parallel)
Sample purity	Required (clogs fluidics)	Tolerates crude lysates
Kinetic resolution	Higher (fast kinetics)	Lower
Mass transport	More sensitive	Less sensitive
Maintenance	High (fluidics)	Low (dip-and-read)

Troubleshooting Matrix

Problem	Mechanism	Solution
Hydrophobic CDRs adsorb to SPR surface	Gold/dextran surface	Add 0.05% Tween-20, use CM7 chip
Aggregation in SPR fluidics	Mass transport artifacts	Filter sample (0.22μm), reduce ligand density
Protein degrades during continuous flow	High instability	Shorter cycle time, add trehalose 5%
Small analyte (<10 kDa) on BLI	Low signal	Use SPR instead
Weak affinity (KD >10μM) on BLI	Fast dissociation	Increase analyte concentration

Mass Transport Considerations

Symptoms of mass transport limitation

Linear association phase (not exponential)
kon varies with ligand density
Rmax varies with flow rate

Mitigation

SPR: Reduce ligand density (<200 RU), increase flow rate (50-100 μL/min)
BLI: Reduce loading (<0.5 nm shift), increase shake speed (1000 rpm)

Regeneration Conditions (SPR)

Condition	Targets	Caution
10 mM Glycine pH 2.0-2.5	Most protein-protein	May denature ligand
1-2 M NaCl	Ionic interactions	Mild, try first
10 mM NaOH	Very stable ligands	Can hydrolyze proteins
10 mM EDTA	His-tag, metal-dependent	Strips Ni-NTA

Kinetic Data Quality Checklist

Reference-subtracted properly
Buffer injection shows flat baseline
Chi² < 10% of Rmax
kon and koff errors < 20%
KD from kinetics matches equilibrium KD (within 3-fold)

Red Flags

kon approaching mass transport limit (>10⁷ M⁻¹s⁻¹)
Rmax >> theoretical maximum (aggregation or avidity)
Large difference between kinetic and equilibrium KD

References

المزيد من هذا المستودع

نفس المستودع

protein-design

BioTender-max/ProteinClaw

Computational protein design toolkit. Use this skill group when: (1) Designing protein binders from scratch, (2) Predicting protein structures (Chai, Boltz, Protenix), (3) Sequence design with ProteinMPNN/LigandMPNN/SolubleMPNN, (4) Quality control and filtering of protein designs, (5) Planning and managing binder design campaigns, (6) Experimental characterization (SPR, BLI, cell-free expression), (7) Searching protein databases (PDB, UniProt, AFDB), (8) Antibody/nanobody design (IgGM, mBER). This is the top-level index. Sub-skills handle specific tools.

2026-03-0411

binder-design

BioTender-max/ProteinClaw

Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen or BindCraft, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types.

2026-03-0411

boltz

BioTender-max/ProteinClaw

Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For Chai prediction, use chai.

2026-03-0411

boltzgen

BioTender-max/ProteinClaw

All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration. For sequence-only design, use proteinmpnn. For structure validation, use boltz.

2026-03-0411

campaign-manager

BioTender-max/ProteinClaw

Goal-oriented binder design campaign planning and health assessment. Use this skill when: (1) Planning a complete binder design campaign, (2) Converting high-level goals into runnable pipelines, (3) Assessing campaign health and pass rates, (4) Diagnosing why designs are failing QC, (5) Estimating time, cost, and expected yields, (6) Selecting between design tools for a specific target. This skill orchestrates the other protein design tools.

2026-03-0411

cell-free-expression

BioTender-max/ProteinClaw

Guidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template design for CFPS, (4) Expressing difficult proteins (disulfide-rich, toxic, membrane).

2026-03-0411

Binding Characterization: SPR and BLI

SPR vs BLI Decision Matrix

Factor

Choose SPR

Choose BLI

Sensitivity

Small molecules (<500 Da)

Large complexes, antibodies

Throughput

Low-medium (serial)

High (96-well parallel)

Sample purity

Required (clogs fluidics)

Tolerates crude lysates

Kinetic resolution

Higher (fast kinetics)

Lower

Mass transport

More sensitive

Less sensitive

Maintenance

High (fluidics)

Low (dip-and-read)

Troubleshooting Matrix

Problem

Mechanism

Solution

Hydrophobic CDRs adsorb to SPR surface

Gold/dextran surface

Add 0.05% Tween-20, use CM7 chip

Aggregation in SPR fluidics

Mass transport artifacts

Filter sample (0.22μm), reduce ligand density

Protein degrades during continuous flow

High instability

Shorter cycle time, add trehalose 5%

Small analyte (<10 kDa) on BLI

Low signal

Use SPR instead

Weak affinity (KD >10μM) on BLI

Fast dissociation

Increase analyte concentration

Mass Transport Considerations

Symptoms of mass transport limitation

Linear association phase (not exponential)

kon varies with ligand density

Rmax varies with flow rate

Mitigation

SPR: Reduce ligand density (<200 RU), increase flow rate (50-100 μL/min)

BLI: Reduce loading (<0.5 nm shift), increase shake speed (1000 rpm)

Regeneration Conditions (SPR)

Condition

Targets

Caution

10 mM Glycine pH 2.0-2.5

Most protein-protein

May denature ligand

1-2 M NaCl

Ionic interactions

Mild, try first

10 mM NaOH

Very stable ligands

Can hydrolyze proteins

10 mM EDTA

His-tag, metal-dependent

Strips Ni-NTA

Kinetic Data Quality Checklist

Reference-subtracted properly

Buffer injection shows flat baseline

Chi² < 10% of Rmax

kon and koff errors < 20%

KD from kinetics matches equilibrium KD (within 3-fold)

Red Flags

kon approaching mass transport limit (>10⁷ M⁻¹s⁻¹)

Rmax >> theoretical maximum (aggregation or avidity)

Large difference between kinetic and equilibrium KD

References