How to read the site
- Map (this page) — pathways as nodes, connected by metabolites. Click a cycle.
- Pathway — that cycle’s enzyme diagram. Click an enzyme.
- Enzyme — the 3D simulator. One catalytic event. References drawer on every page.
Field 1 — Energy metabolism open
Small-molecule conversions. Cytosol, mitochondrial matrix, and inner membrane. Follow the arrows. Each node is a pathway page — the enzyme cards live one layer down.
Cytosol — sugar
Glycolysis
Glucose → pyruvate
10 steps + PFKFB3 · LDH · PDH
▶ OPENGluconeogenesis
Pyruvate → glucose
4 bypasses + 7 reverse cards
▶ OPENPentose phosphate
G6P → NADPH + R5P
returns F6P + GAP
▶ OPENGlycogen
G6P ⇌ branched glycogen
store / break
▶ OPENClick a pathway. The enzyme diagram (glycolysis ↓ · gluconeogenesis ↑ · PPP from G6P) lives on that page.
Mitochondrial matrix — acetyl-CoA hub
Nitrogen — urea cycle
Field 2 — Cell biology same three layers · all layers open
Not a metabolite cycle. A pathway here is a process in time (G1–S–G2–M, a switch flip, a cleavage event). Layer 1 stays this map. Layer 2 is a process page per box below; layer 3 is one simulator per machine, same drawer format, real PDB coordinates. Metabolism cards do not mix onto those pages.
Cell-cycle control
G1 → S → G2 → M · CDK switches
Phosphorylation and its reversal. CDK2 Ser/Thr transfer, Wee1 inhibitory Tyr phosphorylation, Cdc25 dual-specificity phosphatase, CDK7 (CAK, T-loop), PP2A (PPP2CA) metal phosphatase, Separase (ESPL1) Cys cleavage.
6 simulators · process, not a metabolite spiral
CDK2 · CDK7 · Wee1 · Cdc25 · Separase · PP2A
▶ OPEN PROCESS PAGERas GTPase switch
GTP ⇌ GDP switch
Small G-protein on/off. HRas GTP hydrolysis, SOS1 GEF exchange, RASA1 GAP acceleration, PI3K (PIK3CA) lipid kinase, PTEN lipid phosphatase.
5 simulators · PI3K appears only here
HRas · SOS1 · RASA1 · PI3Kα · PTEN
▶ OPEN PROCESS PAGEApoptosis
caspase cascade
Programmed cell death. Casp9 initiator (Cys), Casp3 executioner (Cys), Casp8 extrinsic (Cys), Granzyme B (Ser, different EC). Cytochrome c is referenced from the ETC, not re-simulated.
4 simulators · role split, not chemical split
Casp9 · Casp3 · Casp8 · Granzyme B
▶ OPEN PROCESS PAGESecond messengers
cAMP · cGMP · IP₃ / DAG
Cyclases and hydrolases. Adenylyl cyclase (ATP→cAMP), PDE4 cyclic phosphodiesterase, PLC PIP₂ cleavage, guanylyl cyclase (GTP→cGMP).
4 simulators
Adenylyl cyclase · Guanylyl cyclase · PDE4 · PLC
▶ OPEN PROCESS PAGEHow to read these simulators
Every page shares one visual language. Five ground rules turn that language into honest science — the details of a specific enzyme's motion always live in its own References drawer.
Proposal vs. fact
PROPOSAL markers (amber chips, clickable) and amber-dashed phrases are mechanism inferred from structure + kinetics — not directly observed. Unmarked statements are deposited or measured geometry. Step dots add a third layer: blue = crystal-backed, orange dashed = schematic / transition-state-like, grey = annotation.
Arrow & label language
Gold arrow + moving gold ball = proton (H⁺) path, drawn as a schematic sphere. Blue = attacking nucleophile. Dashed lines = forming / breaking bonds (red/gold = a bond pair changing). Å labels mark the reaction coordinate; the SLOW-MO badge dips the timeline at transition states. Other H atoms are not drawn. Colors always follow the legend at each page's bottom.
Static protein, reconstructed motion
The protein mesh is a static coordinate set — no conformer sampling, thermal motion, or loop dynamics are simulated. Motion interpolates between real crystallographic states; where no crystal exists the pose is schematic and labeled "literature-based", not measured.
Precision vs. accuracy
Printed Å numbers are single values from deposited entries (or our own re-alignment), not measured trajectories. Treat them as plausible crystallographic values; angles read mid-flight are schematic — the chemistry rides on the drawn flight axes, not on every intermediate atom.
Kinetics scope
Each page animates one catalytic event, not a timecourse. No steady-state kinetics, Km/kcat/Vmax·[S], or dynamic equilibria are modeled. Reported constants appear in drawer cards as literature context only — pair the motion with a kinetics chapter for what they mean.
How these simulators are built
- Mechanism research — primary literature via PubMed (kinetic isotope effects, trapped intermediates, transition-state analogs, mutagenesis).
- Structural data — real coordinates from RCSB PDB: apo, Michaelis complex, intermediate and transition-state-analog states are superposed into one frame.
- Ligand geometry — substrates/products from PubChem/PDB chemical component dictionaries.
- Animation — interpolation between real crystallographic states; electron-flow arrows, forming/breaking bonds, residue labels, per-step narration.
Every simulator includes a reference panel linking the exact PDB entries and PMID numbers used.