Directed evolution, bioorthogonal chemistry, click chemistry, PROTACs, unnatural amino acids.
Systems And Chemical Biology Methods
Directed evolution
Iterative mutagenesis + selection/screening to engineer proteins (enzymes, binders) with new functions. Arnold Nobel 2018. Error-prone PCR,…
Click chemistry
Selective bio-orthogonal reactions for in-vivo labelling. CuAAC (Cu-catalysed azide-alkyne cycloaddition) + SPAAC (strain-promoted,…
Bioorthogonal chemistry
Chemistry that proceeds inside living systems without interfering with native biochemistry. Staudinger ligation, tetrazine ligation, SPAAC.…
PROTAC (proteolysis-targeting chimera)
Bifunctional small molecule linking target protein to E3 ubiquitin ligase → degradation via UPS. Catalytic, event-driven pharmacology —…
Unnatural amino acid (UAA) incorporation
Site-specific insertion of non-canonical AAs via orthogonal aaRS/tRNA pair and reassigned stop codon (amber). Enables photocrosslinking,…
Activity-based probe
Small-molecule covalent probe that labels only active/unliganded enzymes. Reports enzyme activity in situ. Cravatt: serine hydrolase ABPs…
Chemical proteomics
MS-based identification of protein targets of small molecules. Affinity pull-downs, thermal proteome profiling (TPP), drug affinity…
CRISPR genetic screen
Genome-wide knockout/activation libraries (GeCKO, Brunello) + phenotypic readout. Pooled or arrayed. Identifies synthetic lethal partners,…
High-throughput screening
Automated assay of ~10⁵-10⁶ compounds against a biological target. Plate-based fluorescence/luminescence. Hit-to-lead to clinical candidate…
Optogenetics
Light-gated ion channels (channelrhodopsin, halorhodopsin) expressed in defined neurons. Millisecond control of activity in vivo.…
Metabolic flux analysis (stoichiometric matrix)
MFA: under quasi-steady-state Sv = 0 with stoichiometric matrix S ∈ R^{m×r} and flux vector v ∈ R^r; underdetermined system constrained by…
CRISPR screen MAGeCK statistics
Li-Köster 2014 MAGeCK: rank-based α-RRA over per-gRNA log fold-changes computes gene-level p-value; negative-binomial dispersion model…
Y2H (Fields-Song 1989)
Fields-Song 1989 yeast-two-hybrid; modern AlphaFold-multimer + AP-MS + cross-linking; protein-interaction network mapping.
RNAi (Fire-Mello 1998)
Fire-Mello 1998 (Nobel 2006) RNA-interference C elegans; modern siRNA-therapy patisiran 2018 first FDA siRNA drug.
CRISPR screen (Shalem 2014)
Shalem-Sanjana-Hartenian 2014 + Wang-Wei 2014 CRISPR-Cas9 genome-wide screens; modern Sabatini + DepMap cancer-dependency.
Chemoproteomics (Cravatt 1999)
B Cravatt 1999 ABPP chemoproteomics; modern ligand-discovery + Backus 2016 covalent-fragment screens.
Nanopore (Deamer-Akeson 1996)
Deamer-Akeson 1996 + Oxford-Nanopore 2014 commercial; modern long-read kbp-Mbp + direct RNA + methylation single-base.
Proximity labeling (Roux 2012)
Roux 2012 BioID + 2018 TurboID + APEX2 Lam 2014; modern in-vivo proximity-proteomics; spatial-proteomics workflow.
Yeast cdc (Hartwell 1971)
L Hartwell 1971 (Nobel 2001) cdc-yeast-screen; modern modern foundational text + chemical-genomics + saturating-mutagenesis Lehner 2024.
Y2H (Fields-Song 1989)
S Fields-O Song 1989 + Bartel 1996 yeast-two-hybrid; modern modern proteome-wide + AP-MS + 2024 cryo-EM-resolved interaction map.
RNAi (Fire-Mello 1998)
A Fire-C Mello 1998 (Nobel 2006) RNA-interference C-elegans; modern modern shRNA / siRNA + miRNA + clinical-launch patisiran 2018.
Chemical genetics (Schreiber 2003)
S Schreiber 2003 'Chemical genetics resulting from a passion'; modern modern foundational + DOS + DEL + 2024 PROTAC + degrader trends.
CRISPRi (Qi 2013)
L Qi-J Weissman 2013 CRISPRi-dCas9; modern modern genome-scale + CRISPRa + CRISPR-screens + 2024 single-cell Perturb-seq.
Optogenetics (Deisseroth 2005)
K Deisseroth-E Boyden 2005 ChR2; modern modern bidirectional + chemogenetics-DREADD Roth 2007 + 2024 ML-driven control.